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Information on EC 1.8.98.6 - formate:CoB-CoM heterodisulfide,ferredoxin reductase
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1.8.98.6 formate:CoB-CoM heterodisulfide,ferredoxin reductaseIUBMB Comments
The enzyme is found in formate-oxidizing CO2-reducing methanogenic archaea such as Methanococcus maripaludis. It consists of a cytoplasmic complex of HdrABC reductase and formate dehydrogenase. Electron pairs donated by formate dehydrogenase are transferred to the HdrA subunit of the reductase, where they are bifurcated, reducing both ferredoxin and CoB-CoM heterodisulfide. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.4, coenzyme F420:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.5, H2:CoB-CoM heterodisulfide,ferredoxin reductase, and EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase.
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The enzyme appears in viruses and cellular organisms
Reaction Schemes
2
+
2
+
+
+
2
=
2
+
2
+
2
+
2
reduced ferredoxin [iron-sulfur] cluster
+
+
+
2
=
2
+
2
oxidized ferredoxin [iron-sulfur] cluster
+
Synonyms
FDH, FdhGHI, formate-driven FBEB, formate: CoMS-S-CoB oxidoreductase, HdrABC-VhuAUGD, HdrDE, HdrDE-FdhGHI, heterodisulfide reductase, heterodisulfide reductase complex, More, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
additional information
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+ = 2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
coenzyme B,coenzyme M,ferredoxin:formate oxidoreductase
The enzyme is found in formate-oxidizing CO2-reducing methanogenic archaea such as Methanococcus maripaludis. It consists of a cytoplasmic complex of HdrABC reductase and formate dehydrogenase. Electron pairs donated by formate dehydrogenase are transferred to the HdrA subunit of the reductase, where they are bifurcated, reducing both ferredoxin and CoB-CoM heterodisulfide. cf. EC 1.8.7.3, ferredoxin:CoB-CoM heterodisulfide reductase, EC 1.8.98.4, coenzyme F420:CoB-CoM heterodisulfide,ferredoxin reductase, EC 1.8.98.5, H2:CoB-CoM heterodisulfide,ferredoxin reductase, and EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
CO2 + reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + H+
formate + oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
-
-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
-
-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
-
-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
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-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
electron flow occurs from formate to CoM-S-S-CoB in the enzyme complex, while methanophenazine (MPhen) derivative is the potential electron carrier in the membranes of Methanonatronarchaeum thermophilum strain AMET1
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-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
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-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
electron flow occurs from formate to CoM-S-S-CoB in the enzyme complex, while methanophenazine (MPhen) derivative is the potential electron carrier in the membranes of Methanonatronarchaeum thermophilum strain AMET1
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?
additional information
?
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the protein complex consists of heterodisulfide reductase, formylmethanofuran dehydrogenase, F420-nonreducing hydrogenase, and formate dehydrogenase. Either H2 or formate can donate electrons to the heterodisulfide-H2 via F420-nonreducing hydrogenase or formate via formate dehydrogenase. When H2 is used as the electron donor for methanogenesis, electrons are transferred to heterodisulfide reductase via F420-nonreducing hydrogenase. Flavin-mediated electron bifurcation at heterodisulfide reductase A then results in reduction of the CoM-S-S-CoB heterodisulfide and a ferredoxin that is used by formylmethanofuran dehydrogenase for the first step in methanogenesis. When hydrogen is limiting or is replaced by formate, formate dehydrogenase is highly expressed and incorporates into the complex. When formate is used as the electron donor for methanogenesis, electrons are transferred to heterodisulfide reductase from formate via formate dehydrogenase
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?
additional information
?
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in Escherichia coli recombinantly expressed Clostridium pasteurianum ferredoxin is used as cosubstrate. The Fdh containing complexes show higher activity with formate compared to hydrogen. The non-FBEB reduction of Fd by Vhu (H2 oxidation) or Fdh (formate oxidation) is not kinetically dominant
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additional information
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in Escherichia coli recombinantly expressed Clostridium pasteurianum ferredoxin is used as cosubstrate. The Fdh containing complexes show higher activity with formate compared to hydrogen. The non-FBEB reduction of Fd by Vhu (H2 oxidation) or Fdh (formate oxidation) is not kinetically dominant
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
CO2 + reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + H+
formate + oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
-
-
-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
-
-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
-
-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
-
-
-
?
2 formate + 2 oxidized ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB
2 CO2 + 2 reduced ferredoxin [iron-sulfur] cluster + CoB + CoM + 2 H+
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-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Fe-S center
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two [4Fe-4S] clusters of the inserted ferredoxin (Fd) domain
additional information
a methanophenazine-like cofactor functions as an electron carrier between the hydrogenase/formate dehydrogenase and the heterodisulfide reductase, cf. EC 1.8.98.1
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
KCl
activates HdrDE activity, best at 3 M KCl, about 50% activity at 2 and 4 M KCl. Formate oxidation by FdhGHI is slightly lower with 2 M KCl instead of NaCl
NaCl
activates FdhGHI activity, best at 2 M, formate oxidation is slightly lower with 2 M KCl instead of NaCl
additional information
at pH 7.5, the specific activity of HdrDE with 2 M potassium chloride is about 40% higher than with 2 M sodium chloride
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
the FBEB specific activity is slightly reduced when 1.6 M phosphate is replaced with 1.5 M phosphate buffer and 100 mM MOPS, although a similar activity is observed in 1.5 M ammonium sulfate and 100 mM MOPS. The FBEB specific activity is significantly reduced in 1.6 M MOPS
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additional information
no inhibition of HdrDE and FdhGHI by diphenyleneiodonium chloride
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
high concentrations of phosphate buffer are required for optimal FBEB activities in vitro, which because they promote hydrophobic protein-protein interactions between the inserted Fd domain on HdrA and Fd
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10.7
CoM-S-S-CoB reduction with methyl viologen as artificial electron donor by HdrDE, membrane fraction, pH 7.5, temperature not specified in the publication, at 2 M KCl
3.3
CoM-S-S-CoB reduction with methyl viologen as artificial electron donor by HdrDE, membrane fraction, pH 8.5, temperature not specified in the publication, at 2 M KCl
5.9
FdhGHI activity on formate with methyl viologen as artificial electron acceptor, membrane fraction, pH 9.5, temperature not specified in the publication, at 2 M NaCl
additional information
thiol production from the reduction in CoM-S-SCoB with formate as electron donor is also measured with a rate of 369 nmol/mg/min under an N2 atmosphere
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5 - 10.5
enzyme activity range, profile overview
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
and strains Mm1264 and Mm1265, derivatives of strain S2 incorporating a poly-His-tag at the C-terminus of HdrB (1264) and at the C-terminus of FdhA (1265), respectively
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CoB-CoM heterodisulfide reductase subunit E; isolated from a hypersaline soda lake
UniProt
brenda
CoB-CoM heterodisulfide reductase subunit E; isolated from a hypersaline soda lake
UniProt
brenda
and strains Mm1264 and Mm1265, derivatives of strain S2 incorporating a poly-His-tag at the C-terminus of HdrB (1264) and at the C-terminus of FdhA (1265), respectively
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-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
Methanonatronarchaeum thermophilum strain AMET1 is able to grow on all tested substrates (methanol, trimethylamine (TMA), dimethylamine (DMA), monomethylamine (MMA)) in combination with formate or molecular hydrogen. Growth parameter during methanogenesis from methylated C1-compounds and formate, overview
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Methanonatronarchaeum thermophilum strain AMET1 is able to grow on all tested substrates (methanol, trimethylamine (TMA), dimethylamine (DMA), monomethylamine (MMA)) in combination with formate or molecular hydrogen. Growth parameter during methanogenesis from methylated C1-compounds and formate, overview
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brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
the catalytic subunit of heterodisulfide reductase (HdrD) is located at the cytoplasmic side of the cytoplasmic membrane. The oxidation of formate is catalyzed by a membrane-bound formate dehydrogenase (FdhGHI)
brenda
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the catalytic subunit of heterodisulfide reductase (HdrD) is located at the cytoplasmic side of the cytoplasmic membrane. The oxidation of formate is catalyzed by a membrane-bound formate dehydrogenase (FdhGHI)
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brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
additional information
metabolism
-
heterodisulfide reductase plays a central role in the methanogenesis cycle of Methanococcus maripaludis. In methanogens without cytochromes, the initial endergonic reduction of CO2 to formylmethanofuran with H2-derived electrons is coupled to the exergonic reduction of a heterodisulfide of coenzymes B and M by flavin-based electron bifurcation (FBEB). Methanococcus maripaludis employs three functional heterodisulfide reductase complexes for FBEB using hydrogen and formate. In Methanococcus maripaludis, FBEB is performed by a heterodisulfide reductase (Hdr) enzyme complex that involves hydrogenase (Vhu), although formate dehydrogenase (Fdh) has been proposed as an alternative to Vhu
metabolism
the oxidation of formate is catalyzed by a membrane-bound formate dehydrogenase (FdhGHI), whereas the oxidation of H2 takes place via a membrane-bound hydrogenase (VhoGAC). Based on this, the electrons fed into the anaerobic respiratory chain by FdhGHI and VhoGAC are subsequently used by a membrane-bound heterodisulfide reductase (HdrDE) to reduce the heterodisulfide (CoM-S-S-CoB), which is the terminal electron acceptor of this system, overview. Three energy-conserving, membrane-bound electron transport systems are known in methanogens: (a) H2: CoMS-S-CoB oxidoreductase (EC 1.8.98.5), (b) coenzyme F420H2: CoMS-S-CoB oxidoreductase (EC 1.8.98.4), and (c) reduced ferredoxin:CoM-S-S-CoB oxidoreductase (EC 1.8.7.3)
metabolism
-
heterodisulfide reductase plays a central role in the methanogenesis cycle of Methanococcus maripaludis. In methanogens without cytochromes, the initial endergonic reduction of CO2 to formylmethanofuran with H2-derived electrons is coupled to the exergonic reduction of a heterodisulfide of coenzymes B and M by flavin-based electron bifurcation (FBEB). Methanococcus maripaludis employs three functional heterodisulfide reductase complexes for FBEB using hydrogen and formate. In Methanococcus maripaludis, FBEB is performed by a heterodisulfide reductase (Hdr) enzyme complex that involves hydrogenase (Vhu), although formate dehydrogenase (Fdh) has been proposed as an alternative to Vhu
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metabolism
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the oxidation of formate is catalyzed by a membrane-bound formate dehydrogenase (FdhGHI), whereas the oxidation of H2 takes place via a membrane-bound hydrogenase (VhoGAC). Based on this, the electrons fed into the anaerobic respiratory chain by FdhGHI and VhoGAC are subsequently used by a membrane-bound heterodisulfide reductase (HdrDE) to reduce the heterodisulfide (CoM-S-S-CoB), which is the terminal electron acceptor of this system, overview. Three energy-conserving, membrane-bound electron transport systems are known in methanogens: (a) H2: CoMS-S-CoB oxidoreductase (EC 1.8.98.5), (b) coenzyme F420H2: CoMS-S-CoB oxidoreductase (EC 1.8.98.4), and (c) reduced ferredoxin:CoM-S-S-CoB oxidoreductase (EC 1.8.7.3)
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physiological function
the energy conservation of Methanonatronarchaeum thermophilum is dependent on a respiratory chain consisting of a hydrogenase (VhoGAC, EC 1.8.98.5), a formate dehydrogenase (FdhGHI, EC 1.8.98.6), and a heterodisulfide reductase (HdrDE) that are well adapted to the harsh physicochemical conditions in the natural habitat. Methanogen Methanonatronarchaeum thermophilum is an extremely haloalkaliphilic and moderately thermophilic archaeon. A methanophenazine-like cofactor might function as an electron carrier between the hydrogenase/formate dehydrogenase and the heterodisulfide reductase. A methanophenazine-like cofactor functions as an electron carrier between the hydrogenase/formate dehydrogenase and the heterodisulfide reductase, cf. EC 1.8.98.1. The electrons fed into the anaerobic respiratory chain by FdhGHI and VhoGAC are subsequently used by a membrane-bound heterodisulfide reductase (HdrDE) to reduce the heterodisulfide (CoM-S-S-CoB), which is the terminal electron acceptor of this system
physiological function
-
the energy conservation of Methanonatronarchaeum thermophilum is dependent on a respiratory chain consisting of a hydrogenase (VhoGAC, EC 1.8.98.5), a formate dehydrogenase (FdhGHI, EC 1.8.98.6), and a heterodisulfide reductase (HdrDE) that are well adapted to the harsh physicochemical conditions in the natural habitat. Methanogen Methanonatronarchaeum thermophilum is an extremely haloalkaliphilic and moderately thermophilic archaeon. A methanophenazine-like cofactor might function as an electron carrier between the hydrogenase/formate dehydrogenase and the heterodisulfide reductase. A methanophenazine-like cofactor functions as an electron carrier between the hydrogenase/formate dehydrogenase and the heterodisulfide reductase, cf. EC 1.8.98.1. The electrons fed into the anaerobic respiratory chain by FdhGHI and VhoGAC are subsequently used by a membrane-bound heterodisulfide reductase (HdrDE) to reduce the heterodisulfide (CoM-S-S-CoB), which is the terminal electron acceptor of this system
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additional information
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when grown on formate as its sole electron donor, Methanococcus maripaludis assembles three Hdr complexes employing two Vhu domains [(Vhu)2Hdr complex], two Fdh domains [(Fdh)2Hdr complex], or one Vhu and one Fdh domain forming a heterocomplex (Fdh/Vhu/Hdr complex). Protein-protein interaction/docking analysis and modeling, usage of the crystal structure of the analogous MvhHdr complex from Methanothermococcus thermolithotrophicus (PDB ID 5ODC) as template, enzyme complex structures comparisons, overview
additional information
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when grown on formate as its sole electron donor, Methanococcus maripaludis assembles three Hdr complexes employing two Vhu domains [(Vhu)2Hdr complex], two Fdh domains [(Fdh)2Hdr complex], or one Vhu and one Fdh domain forming a heterocomplex (Fdh/Vhu/Hdr complex). Protein-protein interaction/docking analysis and modeling, usage of the crystal structure of the analogous MvhHdr complex from Methanothermococcus thermolithotrophicus (PDB ID 5ODC) as template, enzyme complex structures comparisons, overview
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). HDRA_METMP
Methanococcus maripaludis (strain S2 / LL)
658
0
71281
Swiss-Prot
-
HDRB1_METMP
Methanococcus maripaludis (strain S2 / LL)
301
0
33510
Swiss-Prot
-
HDRB2_METMP
Methanococcus maripaludis (strain S2 / LL)
293
0
32026
Swiss-Prot
-
HDRC1_METMP
Methanococcus maripaludis (strain S2 / LL)
192
0
21600
Swiss-Prot
-
HDRC2_METMP
Methanococcus maripaludis (strain S2 / LL)
184
0
20452
Swiss-Prot
-
A0A8B6SDK1_9EURY
441
0
49666
TrEMBL
-
A0A8B3S242_9EURY
382
0
42974
TrEMBL
-
A0A8B3S270_9EURY
141
0
15989
TrEMBL
-
A0A8B3S144_9EURY
198
0
22644
TrEMBL
-
A0A485LW64_9ZZZZ
520
0
56536
TrEMBL
other Location (Reliability: 2)
A0A8B3S0M9_9EURY
755
0
82703
TrEMBL
-
A0A1Y3GAE7_9EURY
276
0
31542
TrEMBL
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
three Hdr complexes employing two Vhu domains [(Vhu)2Hdr complex], two Fdh domains [(Fdh)2Hdr complex], or one Vhu and one Fdh domain forming a heterocomplex (Fdh/Vhu/Hdr complex)
additional information
-
three Hdr complexes employing two Vhu domains [(Vhu)2Hdr complex], two Fdh domains [(Fdh)2Hdr complex], or one Vhu and one Fdh domain forming a heterocomplex (Fdh/Vhu/Hdr complex)
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
nickel affinity column chromatography and Hiprep 16-60 Sephacryl S300HR gel filtration
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recombinant His-tagged enzyme complex components, Fdh, Vhu, and Hdr from Escherichia coli by nickel affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression of His-tagged enzyme complex components, Fdh, Vhu, and Hdr in Escherichia coli
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Costa, K.; Lie, T.; Xia, Q.; Leigh, J.
VhuD facilitates electron flow from H2 or formate to heterodisulfide reductase in Methanococcus maripaludis
J. Bacteriol.
195
5160-5165
2013
Methanococcus maripaludis
brenda
Costa, K.; Wong, P.; Wang, T.; Lie, T.; Dodsworth, J.; Swanson, I.; Burn, J.; Hackett, M.; Leigh, J.
Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase
Proc. Natl. Acad. Sci. USA
107
11050-11055
2010
Methanococcus maripaludis
brenda
Milton, R.; Ruth, J.; Deutzmann, J.; Spormann, A.
Methanococcus maripaludis employs three functional heterodisulfide reductase complexes for flavin-based electron bifurcation using hydrogen and formate
Biochemistry
57
4848-4857
2018
Methanococcus maripaludis, Methanococcus maripaludis LL
brenda
Steiniger, F.; Sorokin, D.; Deppenmeier, U.
Process of energy conservation in the extremely haloalkaliphilic methyl-reducing methanogen Methanonatronarchaeum thermophilum
FEBS J.
289
549-563
2022
Methanonatronarchaeum thermophilum (A0A1Y3GAE7), Methanonatronarchaeum thermophilum AMET1 (A0A1Y3GAE7)
brenda
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Release 2023.1 (January 2023)
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