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Literature summary for 1.8.7.3 extracted from

  • Lubner, C.E.; Peters, J.W.
    Electron bifurcation makes the puzzle pieces fall energetically into place in methanogenic energy conservation (2017), ChemBioChem, 18, 2295-2297 .
    View publication on PubMed

Crystallization (Commentary)

Crystallization (Comment) Organism
analysis of the crystal structure of the Hdr-[NiFe]-hydrogenase complex (HdrABC·MvhAGD) from Methanothermococcus thermolithotrophicus with and without bound heterodisulfide components, overview. The HdrABC·MvhAGD complex is abundant in iron-sulfur cofactors, with 11 [4 Fe-4S] clusters, one [2 Fe-2S], a Ni-Fe site for H2 catalysis, and two noncubane iron-sulfur clusters Methanothermococcus thermolithotrophicus

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ the enzyme is an iron-sulfur subunit A of the HdrABC complex and contains [4 Fe-4S] clusters Methanothermococcus thermolithotrophicus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H+ Methanothermococcus thermolithotrophicus
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2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM
-
?
2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H+ Methanothermococcus thermolithotrophicus DSM 2095
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2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM
-
?
additional information Methanothermococcus thermolithotrophicus Hdr receives two electrons from the oxidation of H2 through MvhAGD [NiFe]-hydrogenase, cf. EC 1.8.98.4 ?
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additional information Methanothermococcus thermolithotrophicus DSM 2095 Hdr receives two electrons from the oxidation of H2 through MvhAGD [NiFe]-hydrogenase, cf. EC 1.8.98.4 ?
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Organism

Organism UniProt Comment Textmining
Methanothermococcus thermolithotrophicus A0A2D0TCB9 CoB-CoM heterodisulfide reductase iron-sulfur subunit A
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Methanothermococcus thermolithotrophicus DSM 2095 A0A2D0TCB9 CoB-CoM heterodisulfide reductase iron-sulfur subunit A
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Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H+
-
Methanothermococcus thermolithotrophicus 2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM
-
?
2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H+
-
Methanothermococcus thermolithotrophicus DSM 2095 2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM
-
?
additional information Hdr receives two electrons from the oxidation of H2 through MvhAGD [NiFe]-hydrogenase, cf. EC 1.8.98.4 Methanothermococcus thermolithotrophicus ?
-
-
additional information Hdr receives two electrons from the oxidation of H2 through MvhAGD [NiFe]-hydrogenase, cf. EC 1.8.98.4 Methanothermococcus thermolithotrophicus DSM 2095 ?
-
-

Subunits

Subunits Comment Organism
More the HdrABC subunits have different catalytic activities and contain the cofactors that comprise the electron-transferring conduits and heterodisulfide binding site, and facilitate the bifurcation of electrons from the sole flavin adenine dinucleotide (FAD) molecule in HdrA Methanothermococcus thermolithotrophicus

Synonyms

Synonyms Comment Organism
CoB-CoM heterodisulfide reductase
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Methanothermococcus thermolithotrophicus
HDR
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Methanothermococcus thermolithotrophicus
heterodisulfide reductase
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Methanothermococcus thermolithotrophicus

Cofactor

Cofactor Comment Organism Structure
FAD the enzyme is an iron-sulfur subunit A of the HdrABC complex and contains [4 Fe-4S] clusters Methanothermococcus thermolithotrophicus
Ferredoxin
-
Methanothermococcus thermolithotrophicus
additional information the HdrABC·MvhAGD (see also EC 1.8.98.1) complex is abundant in iron-sulfur cofactors, with 11 [4 Fe-4S] clusters, one [2 Fe-2S], a Ni-Fe site for H2 catalysis, and two noncubane iron-sulfur clusters Methanothermococcus thermolithotrophicus

General Information

General Information Comment Organism
metabolism a methyl-CoM reductase catalyzes the reductive resolution of methyl-CoM to form methane and a disulfide CoM conjugate of coenzyme B (CoM-S-S-CoB). This is the penultimate conserved step in all pathways of methanogenesis leaving only the reduction of CoM-S-S-CoB and recycling of the key methanogen cofactors CoM and CoB.. The reduction of CoM-S-S-CoB is often coupled to the oxidation of H2, an exergonic reaction with a significant negative free-energy change. Methanogens conserve the free energy by coupling this exergonic reaction to the hydrogen-dependent reduction of ferredoxin, which on its own would be an endergonic reaction. These reactions are coupled through flavin-based electron bifurcation that maximizes the energy efficiency in hydrogenotrophic methanogenesis. Heterodisulfide reductase (Hdr) is the valve that closes the cycle of methanogenesis, allowing energy to be conserved and providing an energetic advantage to the cell. Hdr catalyzes flavin-based electron bifurcation that results in the exergonic reduction of heterodisulfide (CoMS-S-CoB) coupled to the endergonic reduction of ferredoxin. In the proposed mechanism of bifurcation, the bifurcation-site flavin receives two electrons from a single donor, and then bifurcate one electron to reduce the heterodisulfide and one electron to reduce ferredoxin. Another round of bifurcation results in the complete reduction of CoM-S-S-CoB to HS-CoB and HS-CoM and 2 equivalents of reduced ferredoxin. Hdr receives two electrons from the oxidation of H2 through MvhAGD [NiFe]-hydrogenase EC 1.8.98.4 Methanothermococcus thermolithotrophicus
additional information the HdrABC subunits have different catalytic activities and contain the cofactors that comprise the electron-transferring conduits and heterodisulfide binding site, and facilitate the bifurcation of electrons from the sole flavin adenine dinucleotide (FAD) molecule in HdrA, see also EC 1.8.98.1, EC 1.8.98.4, and EC 1.8.98.5. The unusual noncubane iron-sulfur clusters are observed to bind and catalyze the reduction of CoM-S-S-CoB, and, based on crystal-soaking experiments with the disulfide, HS-CoB dissociates first after reduction from the first round of bifurcation. HS-CoM then dissociates after reduction from the second round of bifurcation. Structure-function relationship, overview Methanothermococcus thermolithotrophicus
physiological function heterodisulfide reductase (Hdr) is the valve that closes the cycle of methanogenesis, allowing energy to be conserved and providing an energetic advantage to the cell. Hdr catalyzes flavin-based electron bifurcation that results in the exergonic reduction of heterodisulfide (CoMS-S-CoB) coupled to the endergonic reduction of ferredoxin. In the proposed mechanism of bifurcation, the bifurcation-site flavin receives two electrons from a single donor, and then bifurcate one electron to reduce the heterodisulfide and one electron to reduce ferredoxin. Another round of bifurcation results in the complete reduction of CoM-S-S-CoB to HS-CoB and HS-CoM and 2 equivalents of reduced ferredoxin Methanothermococcus thermolithotrophicus