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Catalytic Site Atlas

CSA LITERATURE entry for 1mro

E.C. namecoenzyme-B sulfoethylthiotransferase
SpeciesMethanobacterium thermoautotrophicum (Bacteria)
E.C. Number (IntEnz) 2.8.4.1
CSA Homologues of 1mro1e6v,1e6y,1hbm,1hbn,1hbo,1hbu,
CSA Entries With UniProtID P11558
CSA Entries With EC Number 2.8.4.1
PDBe Entry 1mro
PDBSum Entry 1mro
MACiE Entry M0156

Literature Report

IntroductionMethyl coenzyme M Reductase is responsible for the last step in methane production by methanogenic archaea. It utilises the ability of Nickel to adopt oxidation states I, II and III in order to catalyse the conversion of methyl coenzyme M and methyl coenzyme B to give methane and a heterodisulphide compound between the two coenzymes, in a complex redox cycle. The enzyme, like many found in archaea, is able to withstand high temperatures and salt content.
MechansimThe reaction proceeds in a cycle. Starting with the activation of coenzyme B by Asn 501, a thiolpeptide bond between Gly A465 and Tyr A466 accepts a single electron from the sulphur atom of coenzyme B to form a thioketyl radical that reduces Ni(III) bound to a methyl group to Ni (II). Protonation by Tyrosine B367 then occurs resulting in methane release. Meanwhile the coenzyme B radical reacts with methyl coenzyme M forming a methylcoM-coB disulphide radical. This in turn loses its methyl group to Ni (I), the oxidation state of the enzyme when no substrate is bound, forming methyl bound Ni (II) and generating a disulphide anion radical which reduces the Ni (II) previously generated to Ni (I) so that it can accept the methyl group and continue the cycle.
Reaction

Catalytic Sites for 1mro

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyA465465macie:sideChainThe peptide bond between Gly 465 and Tyr 466 is modified to contain a sulphur atom in place of a nitrogen; thus it can accept an electron from coenzyme M to form a thioketyl radical which then in turn passes the electron to Ni(III), reducing it.
AspA501501macie:sideChainActs to activate coenzyme B by deprotonation so that it can donate an electron to the thiopeptide bond and subsequently react with methylcoenzyme M.
TyrB367367macie:sideChainProtonates methyl group attached to Nickel cofactor resulting in the release of methane and the regeneration of Ni(I) to complete the redox cycle.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyD465465macie:sideChainThe peptide bond between Gly 465 and Tyr 466 is modified to contain a sulphur atom in place of a nitrogen; thus it can accept an electron from coenzyme M to form a thioketyl radical which then in turn passes the electron to Ni(III), reducing it.
AspD501501macie:sideChainActs to activate coenzyme B by deprotonation so that it can donate an electron to the thiopeptide bond and subsequently react with methylcoenzyme M.
TyrE367367macie:sideChainProtonates methyl group attached to Nickel cofactor resulting in the release of methane and the regeneration of Ni(I) to complete the redox cycle.

Literature References

Notes:
Grabarse W
Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation.
J Mol Biol 2000 303 329-344
PubMed: 11023796
Grabarse W
On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding.
J Mol Biol 2001 309 315-330
PubMed: 11491299
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