Coenzyme-B sulfoethylthiotransferase

 

Methyl 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.

 

Reference Protein and Structure

Sequences
P11558 UniProt (2.8.4.1)
P11560 UniProt (2.8.4.1)
P11562 UniProt (2.8.4.1) IPR016212 (Sequence Homologues) (PDB Homologues)
Biological species
Methanothermobacter marburgensis str. Marburg (Archaea) Uniprot
PDB
1mro - METHYL-COENZYME M REDUCTASE (1.16 Å) PDBe PDBsum 1mro
Catalytic CATH Domains
3.30.70.470 CATHdb 1.20.840.10 CATHdb (see all for 1mro)
Cofactors
Coenzyme f430 (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:2.8.4.1)

methyl-CoM(1-)
CHEBI:58286ChEBI
+
coenzyme B(3-)
CHEBI:58596ChEBI
→
CoM-S-S-CoB(4-)
CHEBI:58411ChEBI
+
methane
CHEBI:16183ChEBI
Alternative enzyme names: Methyl coenzyme M reductase, Methyl-CoM reductase,

Enzyme Mechanism

Introduction

The reaction proceeds in a cycle. Starting with the activation of coenzyme B by Asn481D, a thiolpeptide bond between Gly445D and Tyr466D 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 Tyrosine367E 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.

Catalytic Residues Roles

UniProt PDB* (1mro)
Gln147 Gln147(146)A Forms part of the nickel binding site. metal ligand, electrostatic stabiliser
Tyr333 Tyr333(332)D Helps stabilise the reactive intermediates and transition states formed during the course of the reaction. radical stabiliser, electrostatic stabiliser
Gly445 (ptm) Gly445(444)D (ptm) The peptide bond between Gly445 and Tyr446 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. single electron relay, single electron acceptor, single electron donor
Tyr367 Tyr367(366)E Protonates methyl group attached to Nickel cofactor resulting in the release of methane and the regeneration of Ni(I) to complete the redox cycle. proton acceptor, proton donor, proton relay, electrostatic stabiliser, radical stabiliser
Asn481 Asn481(480)D Acts to activate coenzyme B by deprotonation so that it can donate an electron to the thiopeptide bond and subsequently react with methylcoenzyme M. proton relay, proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic substitution, proton transfer, overall reactant used, cofactor used, coordination to a metal ion, intermediate formation, redox reaction, radical formation, heterolysis, overall product formed, decoordination from a metal ion, proton relay, coordination, radical propagation, electron transfer, radical termination, native state of cofactor regenerated, intermediate terminated, native state of enzyme regenerated

References

  1. Ermler U (2005), Dalton Trans, 3451-3458. On the mechanism of methyl-coenzyme M reductase. DOI:10.1039/b506697b. PMID:16234924.
  2. Shima S (2016), Angew Chem Int Ed Engl, 55, 13648-13649. The Biological Methane-Forming Reaction: Mechanism Confirmed Through Spectroscopic Characterization of a Key Intermediate. DOI:10.1002/anie.201606269. PMID:27571920.
  3. Wongnate T et al. (2015), J Biol Chem, 290, 9322-9334. The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order. DOI:10.1074/jbc.M115.636761. PMID:25691570.
  4. Cedervall PE et al. (2011), J Am Chem Soc, 133, 5626-5628. Structural analysis of a Ni-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis. DOI:10.1021/ja110492p. PMID:21438550.
  5. Dey M et al. (2010), Biochemistry, 49, 10902-10911. Detection of organometallic and radical intermediates in the catalytic mechanism of methyl-coenzyme M reductase using the natural substrate methyl-coenzyme M and a coenzyme B substrate analogue. DOI:10.1021/bi101562m. PMID:21090696.
  6. Cedervall PE et al. (2010), Biochemistry, 49, 7683-7693. Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues . DOI:10.1021/bi100458d. PMID:20707311.
  7. Chen SL et al. (2009), J Am Chem Soc, 131, 9912-9913. Is there a Ni-methyl intermediate in the mechanism of methyl-coenzyme M reductase? DOI:10.1021/ja904301f. PMID:19569621.
  8. Harmer J et al. (2008), J Am Chem Soc, 130, 10907-10920. A nickel hydride complex in the active site of methyl-coenzyme m reductase: implications for the catalytic cycle. DOI:10.1021/ja710949e. PMID:18652465.
  9. Duin EC et al. (2008), J Phys Chem B, 112, 2466-2482. A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations. DOI:10.1021/jp709860c. PMID:18247503.
  10. Goenrich M et al. (2004), J Biol Inorg Chem, 9, 691-705. Probing the reactivity of Ni in the active site of methyl-coenzyme M reductase with substrate analogues. DOI:10.1007/s00775-004-0552-1. PMID:15365904.
  11. Pelmenschikov V et al. (2002), J Am Chem Soc, 124, 4039-4049. A Mechanism from Quantum Chemical Studies for Methane Formation in Methanogenesis. DOI:10.1021/ja011664r. PMID:11942842.
  12. Grabarse W et al. (2001), J Mol Biol, 309, 315-330. On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding. DOI:10.1006/jmbi.2001.4647. PMID:11491299.
  13. Grabarse W et al. (2000), J Mol Biol, 303, 329-344. Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation. DOI:10.1006/jmbi.2000.4136. PMID:11023796.

Step 1. Nickel (Ni(I)) of factor 430 attacks the methyl group of the methylated coenzyme M, which is reprotonated from Tyr367E. Nickel assumed the Ni(III) oxidation state.

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Catalytic Residues Roles

Residue Roles
Gln147(146)A metal ligand
Tyr333(332)D electrostatic stabiliser
Tyr367(366)E proton donor

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, overall reactant used, cofactor used, coordination to a metal ion, intermediate formation

Step 2. Tyr367E is inferred to deprotonate coenzyme M, causing it to donate a single electron to the Ni(III) ion of factor 430.

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Catalytic Residues Roles

Residue Roles
Gln147(146)A metal ligand, electrostatic stabiliser
Gly445(444)D (ptm) single electron donor, single electron acceptor
Tyr333(332)D electrostatic stabiliser
Gly445(444)D (ptm) single electron relay
Tyr367(366)E proton acceptor

Chemical Components

proton transfer, redox reaction, radical formation, intermediate formation

Step 3. The methyl group deprotonates Tyr367E whilst disassociating from Ni(II) in factor 430. Asn481D deprotonates coenzyme B and, in turn, is deprotonated by Tyr367E.

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Catalytic Residues Roles

Residue Roles
Gln147(146)A metal ligand
Tyr333(332)D radical stabiliser
Asn481(480)D proton relay
Tyr367(366)E proton relay
Asn481(480)D proton acceptor, proton donor
Tyr367(366)E proton acceptor, proton donor

Chemical Components

proton transfer, heterolysis, overall reactant used, intermediate formation, overall product formed, decoordination from a metal ion, proton relay

Step 4. The thiolate of coenzyme B attacks the thiyl radical of coenzyme M in a coordination reaction.

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Catalytic Residues Roles

Residue Roles
Gln147(146)A metal ligand
Tyr333(332)D radical stabiliser
Tyr367(366)E radical stabiliser

Chemical Components

coordination, radical propagation, intermediate formation

Step 5. The thiyl radical of coenzyme M donates a second electron to the nickel of factor 430, regenerating the Ni(I) oxidation state.

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Catalytic Residues Roles

Residue Roles
Gln147(146)A metal ligand
Gly445(444)D (ptm) single electron donor, single electron acceptor
Tyr333(332)D electrostatic stabiliser
Tyr367(366)E electrostatic stabiliser
Gly445(444)D (ptm) single electron relay

Chemical Components

electron transfer, radical termination, overall product formed, native state of cofactor regenerated, intermediate terminated, native state of enzyme regenerated
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Step 1. Nickel (Ni(I)) of factor 430 attacks the methyl group of the methylated coenzyme M, which is reprotonated from Tyr367E. Nickel assumed the Ni(III) oxidation state.

Step 2. Tyr367E is inferred to deprotonate coenzyme M, causing it to donate a single electron to the Ni(III) ion of factor 430.

Step 3. The methyl group deprotonates Tyr367E whilst disassociating from Ni(II) in factor 430. Asn481D deprotonates coenzyme B and, in turn, is deprotonated by Tyr367E.

Step 4. The thiolate of coenzyme B attacks the thiyl radical of coenzyme M in a coordination reaction.

Step 5. The thiyl radical of coenzyme M donates a second electron to the nickel of factor 430, regenerating the Ni(I) oxidation state.

Products.

Introduction

This mechanism proposal assumes that the first step is the attack by the Ni(I) on the thioether sulfur of methyl-coenzyme M. This yields a free methyl radical which reacts with the thiol group of coenzyme B to give methane and the coenzyme B thiyl radical [PMID:11942842]. This radical then attacks the CoM sulfur, forming the final product and regenerating the cofactor.

Catalytic Residues Roles

UniProt PDB* (1mro)
Gln147 Gln147(146)A Forms part of the nickel binding site. metal ligand
Gly445 (ptm) Gly445(444)D (ptm) The 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(II), reducing it. single electron relay, single electron acceptor, single electron donor
Tyr333, Tyr367 Tyr333(332)D, Tyr367(366)E Helps stabilise the reactive intermediates and transition states formed during the course of the reaction. electrostatic stabiliser
Asn481 Asn481(480)D Acts to activate coenzyme B. activator, electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

overall reactant used, cofactor used, coordination to a metal ion, intermediate formation, electron transfer, homolysis, hydrogen transfer, colligation, bimolecular homolytic addition, native state of cofactor regenerated, native state of enzyme regenerated, overall product formed

References

  1. Pelmenschikov V et al. (2002), J Am Chem Soc, 124, 4039-4049. A Mechanism from Quantum Chemical Studies for Methane Formation in Methanogenesis. DOI:10.1021/ja011664r. PMID:11942842.
  2. Wongnate T et al. (2016), Science, 352, 953-958. The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase. DOI:10.1126/science.aaf0616. PMID:27199421.
  3. Shima S (2016), Angew Chem Int Ed Engl, 55, 13648-13649. The Biological Methane-Forming Reaction: Mechanism Confirmed Through Spectroscopic Characterization of a Key Intermediate. DOI:10.1002/anie.201606269. PMID:27571920.
  4. Wongnate T et al. (2015), J Biol Chem, 290, 9322-9334. The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order. DOI:10.1074/jbc.M115.636761. PMID:25691570.
  5. Scheller S et al. (2013), J Am Chem Soc, 135, 14975-14984. Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on the formation and anaerobic oxidation of methane. DOI:10.1021/ja406485z. PMID:24004388.
  6. Ebner S et al. (2010), J Am Chem Soc, 132, 567-575. Binding of coenzyme B induces a major conformational change in the active site of methyl-coenzyme M reductase. DOI:10.1021/ja906367h. PMID:20014831.
  7. Craft JL et al. (2004), J Am Chem Soc, 126, 4068-4069. Nickel oxidation states of F(430) cofactor in methyl-coenzyme M reductase. DOI:10.1021/ja038082p. PMID:15053571.

Step 1. Nickel (Ni(I)) of factor 430 attacks the sulfur atom of the methylated coenzyme M, forming a methyl radical and Ni(II).

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Catalytic Residues Roles

Residue Roles
Gln147(146)A metal ligand
Tyr367(366)E electrostatic stabiliser
Tyr333(332)D electrostatic stabiliser
Gly445(444)D (ptm) single electron acceptor, single electron donor, single electron relay

Chemical Components

overall reactant used, cofactor used, coordination to a metal ion, intermediate formation, electron transfer, homolysis

Step 2. The methyl radical abstracts a proton from the CoB substrate.

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Catalytic Residues Roles

Residue Roles
Tyr333(332)D electrostatic stabiliser
Tyr367(366)E electrostatic stabiliser
Gln147(146)A metal ligand
Asn481(480)D activator

Chemical Components

hydrogen transfer

Step 3. The CoB radical then initiates a coligation with the CoM radical, forming the final intermediate.

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Catalytic Residues Roles

Residue Roles
Tyr333(332)D electrostatic stabiliser
Tyr367(366)E electrostatic stabiliser

Chemical Components

colligation, ingold: bimolecular homolytic addition

Step 4. The reactive intermediate transfers the excess electron back to the Ni(II) centre, regenerating the active site.

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Catalytic Residues Roles

Residue Roles
Gln147(146)A metal ligand
Asn481(480)D electrostatic stabiliser
Tyr333(332)D electrostatic stabiliser
Tyr367(366)E electrostatic stabiliser

Chemical Components

electron transfer, native state of cofactor regenerated, native state of enzyme regenerated, overall product formed
Download: Image, Marvin File

Step 1. Nickel (Ni(I)) of factor 430 attacks the sulfur atom of the methylated coenzyme M, forming a methyl radical and Ni(II).

Step 2. The methyl radical abstracts a proton from the CoB substrate.

Step 3. The CoB radical then initiates a coligation with the CoM radical, forming the final intermediate.

Step 4. The reactive intermediate transfers the excess electron back to the Ni(II) centre, regenerating the active site.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid