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Literature summary extracted from

  • Guan, H.H.; Hsieh, Y.C.; Lin, P.J.; Huang, Y.C.; Yoshimura, M.; Chen, L.Y.; Chen, S.K.; Chuankhayan, P.; Lin, C.C.; Chen, N.C.; Nakagawa, A.; Chan, S.I.; Chen, C.J.
    Structural insights into the electron/proton transfer pathways in the quinol fumarate reductase from Desulfovibrio gigas (2018), Sci. Rep., 8, 14935 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.3.5.1 purified native enzyme, hanging drop vapour diffusion method, mixing of 0.001 ml of protein solution and 0.001 ml of reservoir solution, and equilibration against 0.15 ml of reservoir solution containing 100 mM NaCl, 28% PEG 4000, and 100 mM Tris, pH 8.5, at 18 °C for two weeks, X-ray diffraction structure determination and analysis at resolution 3.6 A, molecular replacement method using the structure of QFR from Wolinella succinogenes (PDB ID 2BS2) without redox cofactors as the search model, modelling Megalodesulfovibrio gigas
7.1.1.12 hanging-drop vapor-diffusion method, crystal structure is determined at 3.6 A resolution Megalodesulfovibrio gigas

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.3.5.1 membrane quinol:fumarate reductase (QFR) is an integral membrane protein Megalodesulfovibrio gigas 16020
-
7.1.1.12 membrane
-
 Megalodesulfovibrio gigas 16020
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
7.1.1.12 Fe-S cluster the enzyme contains three iron-sulfur clusters Megalodesulfovibrio gigas

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.3.5.1 succinate + menaquinone Megalodesulfovibrio gigas
-
 fumarate + menaquinol
-
 ?
1.3.5.1 succinate + menaquinone Megalodesulfovibrio gigas DSM 1382
-
 fumarate + menaquinol
-
 ?
7.1.1.12 fumarate + menaquinol + 2 H+[side 2] Megalodesulfovibrio gigas in the anaerobic respiratory chain succinate + menaquinone + 2 H+[side 1]
-
 r
7.1.1.12 fumarate + menaquinol + 2 H+[side 2] Megalodesulfovibrio gigas ATCC 19364 in the anaerobic respiratory chain succinate + menaquinone + 2 H+[side 1]
-
 r
7.1.1.12 succinate + menaquinone + 2 H+[side 1] Megalodesulfovibrio gigas
-
 fumarate + menaquinol + 2 H+[side 2]
-
 r
7.1.1.12 succinate + menaquinone + 2 H+[side 1] Megalodesulfovibrio gigas ATCC 19364
-
 fumarate + menaquinol + 2 H+[side 2]
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.3.5.1 Megalodesulfovibrio gigas T2G9X8
-
-
1.3.5.1 Megalodesulfovibrio gigas DSM 1382 T2G9X8
-
-
7.1.1.12 Megalodesulfovibrio gigas T2G9X8 AND T2GAT5 AND T2GB49 T2G9X8: iron-sulfur subunit, T2GAT5: cytochrome b subunit, T2GB49: flavoprotein subunit
-
7.1.1.12 Megalodesulfovibrio gigas ATCC 19364 T2G9X8 AND T2GAT5 AND T2GB49 T2G9X8: iron-sulfur subunit, T2GAT5: cytochrome b subunit, T2GB49: flavoprotein subunit
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.3.5.1 native enzyme from cell-free supernatant of cell extract by anion exchange chromatography, dialysis, and another anion exchange chromatography, followed gel filtration and ultrafiltration Megalodesulfovibrio gigas
7.1.1.12
-
 Megalodesulfovibrio gigas

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.3.5.1 additional information analysis of the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas, overview Megalodesulfovibrio gigas ?
-
-
1.3.5.1 additional information analysis of the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas, overview Megalodesulfovibrio gigas DSM 1382 ?
-
-
1.3.5.1 succinate + menaquinone
-
 Megalodesulfovibrio gigas fumarate + menaquinol
-
 ?
1.3.5.1 succinate + menaquinone
-
 Megalodesulfovibrio gigas DSM 1382 fumarate + menaquinol
-
 ?
7.1.1.12 fumarate + menaquinol + 2 H+[side 2] in the anaerobic respiratory chain Megalodesulfovibrio gigas succinate + menaquinone + 2 H+[side 1]
-
 r
7.1.1.12 fumarate + menaquinol + 2 H+[side 2] in the anaerobic respiratory chain Megalodesulfovibrio gigas ATCC 19364 succinate + menaquinone + 2 H+[side 1]
-
 r
7.1.1.12 succinate + menaquinone + 2 H+[side 1]
-
 Megalodesulfovibrio gigas fumarate + menaquinol + 2 H+[side 2]
-
 r
7.1.1.12 succinate + menaquinone + 2 H+[side 1]
-
 Megalodesulfovibrio gigas ATCC 19364 fumarate + menaquinol + 2 H+[side 2]
-
 r

Subunits

EC Number Subunits Comment Organism
1.3.5.1 homodimer QFR is a homodimer, each protomer comprising two hydrophilic subunits, A and B, and one transmembrane subunit C, together with six redox cofactors including two b-hemes. One menaquinone molecule is bound near heme bL in the hydrophobic subunit C. Two heterotrimeric complexes, each comprising subunits A, B and C, form one stable homodimer (A2B2C2) with major contacts between two C subunit. The formation of the homo-dimer, (A2B2C2), arises from contact of the two C subunits Megalodesulfovibrio gigas
7.1.1.12 homodimer each protomer comprising two hydrophilic subunits, A and B, and one transmembrane subunit C Megalodesulfovibrio gigas

Synonyms

EC Number Synonyms Comment Organism
1.3.5.1 fdrB
-
 Megalodesulfovibrio gigas
1.3.5.1 QFR
-
 Megalodesulfovibrio gigas
1.3.5.1 quinol:fumarate reductase
-
 Megalodesulfovibrio gigas

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.3.5.1 37
-
 assay at Megalodesulfovibrio gigas

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.3.5.1 7.6
-
 assay at Megalodesulfovibrio gigas

Cofactor

EC Number Cofactor Comment Organism Structure
1.3.5.1 heme b two b-hemes are bound per homodimer Megalodesulfovibrio gigas
1.3.5.1 menaquinone one menaquinone molecule is bound near heme bL in the hydrophobic subunit C Megalodesulfovibrio gigas
7.1.1.12 FAD covalently bound Megalodesulfovibrio gigas
7.1.1.12 Fe-S cluster the enzyme contains three iron-sulfur clusters Megalodesulfovibrio gigas
7.1.1.12 heme the enzyme contains two heme b groups Megalodesulfovibrio gigas

General Information

EC Number General Information Comment Organism
1.3.5.1 evolution one menaquinone molecule is bound near heme bL in the hydrophobic subunit C. This location of the menaquinone-binding site differs from the menaquinol-binding cavity proposed previously for QFR from Wolinella succinogenes. The observed bound menaquinone might serve as an additional redox cofactor to mediate the proton-coupled electron transport across the membrane Megalodesulfovibrio gigas
1.3.5.1 metabolism QFR catalyzes the coupled reduction of fumarate to succinate with the oxidation of hydroquinone (quinol) to quinone on opposite sides of the inner cytoplasmic membrane. The reverse reaction, namely, the coupled oxidation of succinate to fumarate with the reduction of quinone to quinol, is catalyzed by the well-studied succinate:quinone reductase (SQR, EC 1.3.5.1), often referred to as complex II in the respiratory electron-transport chain of aerobic organisms Megalodesulfovibrio gigas
1.3.5.1 additional information quinol:fumarate reductase (QFR) is an integral membrane protein with three subunits: a flavoprotein (subunit A), an iron-sulphur protein (subunit B), and a membrane-embedded subunit (subunit C) Megalodesulfovibrio gigas
1.3.5.1 physiological function the membrane-embedded quinol:fumarate reductase (QFR) in anaerobic bacteria catalyzes the reduction of fumarate to succinate by quinol in the anaerobic respiratory chain Megalodesulfovibrio gigas