Information on EC 1.1.5.6 - formate dehydrogenase-N

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
1.1.5.6
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RECOMMENDED NAME
GeneOntology No.
formate dehydrogenase-N
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
formate + a quinone = CO2 + a quinol
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
formate to dimethyl sulfoxide electron transfer
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formate to nitrite electron transfer
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formate to trimethylamine N-oxide electron transfer
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nitrate reduction III (dissimilatory)
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SYSTEMATIC NAME
IUBMB Comments
formate:quinone oxidoreductase
The enzyme contains molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters and two heme b groups. Formate dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the menaquinone pool in the cytoplasmic membrane to a dissimilatory nitrate reductase (EC 1.7.5.1), which transfers electrons to nitrate in the cytoplasm. The system generates proton motive force under anaerobic conditions [3].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
formate + 2,3-dimethoxy-5-methyl-6-(farnesylfarnesyl)-1,4-benzoquinone
CO2 + ?
show the reaction diagram
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?
formate + 2,3-dimethyl-1,4-naphthoquinone
CO2 + 2,3-dimethyl-l,4-naphthoquinol
show the reaction diagram
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?
formate + 2,6-dichlorophenolindophenol
CO2 + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
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dichlorophenylindophenol reduction in presence of phenazine methosulfate
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ir
formate + a quinone
CO2 + a quinol
show the reaction diagram
formate + benzyl viologen
CO2 + reduced benzyl viologen
show the reaction diagram
formate + ferricyanide
CO2 + ferrocyanide + H+
show the reaction diagram
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?
formate + menaquinone
?
show the reaction diagram
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?
formate + menaquinone
CO2 + menaquinol
show the reaction diagram
formate + methyl viologen
CO2 + reduced methyl viologen
show the reaction diagram
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-
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ir
formate + methylene blue
CO2 + reduced methylene blue
show the reaction diagram
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-
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?
formate + nitroblue tetrazolium
CO2 + reduced nitroblue tetrazolium
show the reaction diagram
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?
additional information
?
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the mRNA specifying the first 17 codons of fdnG forms a stable stem-loop structure that is important in modulating FDH-N translation
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
formate + a quinone
CO2 + a quinol
show the reaction diagram
formate + menaquinone
?
show the reaction diagram
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?
formate + menaquinone
CO2 + menaquinol
show the reaction diagram
P24183 and P0AAJ3 and P0AEK7
Fdh-N and dissimilatory nitrate reductase (Nar) can form a redox loop where proton motive force generation is best described as the sum of the following two effects. 1. Two protons, which are taken up from the cytoplasm at the Fdh-N menaquinone reduction site, are translocated across the membrane and released to the periplasm from the menaquinol oxidation site in Nar. 2. Two electrons are transferred from the formate oxidation site in periplasm to the NO3- reduction site in cytoplasm. This is not accompanied by an actual proton translocation across the membrane but generates a membrane potential, which is equivalent to 2 H+ translocation across the membrane. The result is consistent with the measured ratio of proton translocation to electron transfer in this system. In the catalytic site, the Mo directly takes up electrons from the bound substrate. These electrons are transferred to the beta subunit though the [4Fe4S] cluster (FeS-0) in the alpha subunit. The four [4Fe-4S] clusters in the beta subunit, which are aligned in the order of FeS-1, FeS-4, FeS-2, and FeS-3, connect the alpha and gamma subunits like an electric wire. From FeS-3 of the beta subunit, electrons are transferred to heme bP (P for periplasm) in the gamma subunit and then across the membrane to heme bC (C for cytoplasm). Menaquinone binds to a histidine ligand (Hisg169) of heme bC and can directly accept electrons through this residue. The electron transfer from formate (standard redox potential, 2420 mV) to menaquinone (275 mV) is a highly exergonic reaction, allowing the electron transfer against the membrane potential
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?
additional information
?
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the mRNA specifying the first 17 codons of fdnG forms a stable stem-loop structure that is important in modulating FDH-N translation
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
P24183 and P0AAJ3 and P0AEK7
the structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 A through the enzyme. In the catalytic site, the Mo directly takes up electrons from the bound substrate. These electrons are transferred to the beta subunit through the [4Fe4S] cluster (FeS-0) in the alpha subunit. The four [4Fe-4S] clusters in the beta subunit, which are aligned in the order of FeS-1, FeS-4, FeS-2, and FeS-3, connect the alpha and gamma subunits like an electric wire. From FeS-3 of the beta subunit, electrons are transferred to heme bP (P for periplasm) in the gamma subunit and then across the membrane to heme bC (C for cytoplasm). Menaquinone binds to a histidine ligand (Hisg169) of heme bC and can directly accept electrons through this residue
cytochrome b
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the low-potential cytochrome b of the formate dehydrogenase complex is an essential component in the electron transport from formate to menaquinone. The 25000 Da subunit represents cytochrome b
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cytochrome b556
P24183 and P0AAJ3 and P0AEK7
FdnI encodes cytochrome b556
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heme
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the enzyme contains (in relative molar amounts): 1.0 heme, 0.95 molybdenum, 0.96 selenium, 14 non-heme iron, and 13 acid-labile sulfide
heme b
P24183 and P0AAJ3 and P0AEK7
the structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 A through the enzyme. In the catalytic site, the Mo directly takes up electrons from the bound substrate. These electrons are transferred to the beta subunit through the [4Fe4S] cluster (FeS-0) in the alpha subunit. The four [4Fe-4S] clusters in the beta subunit, which are aligned in the order of FeS-1, FeS-4, FeS-2, and FeS-3, connect the alpha and gamma subunits like an electric wire. From FeS-3 of the beta subunit, electrons are transferred to heme bP (P for periplasm) in the gamma subunit and then across the membrane to heme bC (C for cytoplasm). Menaquinone binds to a histidine ligand (Hisg169) of heme bC and can directly accept electrons through this residue
menaquinone
P24183 and P0AAJ3 and P0AEK7
the structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 A through the enzyme. In the catalytic site, the Mo directly takes up electrons from the bound substrate. These electrons are transferred to the beta subunit through the [4Fe4S] cluster (FeS-0) in the alpha subunit. The four [4Fe-4S] clusters in the beta subunit, which are aligned in the order of FeS-1, FeS-4, FeS-2, and FeS-3, connect the alpha and gamma subunits like an electric wire. From FeS-3 of the beta subunit, electrons are transferred to heme bP (P for periplasm) in the gamma subunit and then across the membrane to heme bC (C for cytoplasm). Menaquinone binds to a histidine ligand (Hisg169) of heme bC and can directly accept electrons through this residue
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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contains neither FAD nor FMN
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cyanide
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iodoacetamide
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p-hydroxymercuribenzoate
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.12
formate
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30°C, per mol of heme
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
563
formate
Escherichia coli
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30°C, per mol of heme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25000
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x * 110000 + x * 25000 + x * 20000, SDS-PAGE
32000
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x * 110000 (alpha) + x * 32000 (beta) + x * 20000 (gamma), the molar ratio of alpha:beta:gamma is 1:1.2:0.55, SDS-PAGE
110000
590000
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gel filtration
additional information
P24183 and P0AAJ3 and P0AEK7
the complete nucleotide sequence of the formate dehydrogenase-N structural gene operon is reported
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
trimer
P24183 and P0AAJ3 and P0AEK7
alpha and beta subunits of Fdh-N are on the periplasmic side of the membrane
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure at 1.6 A
P24183 and P0AAJ3 and P0AEK7
hanging-drop vapour-diffusion technique. Crystals of Fdh-N belong to the cubic space group P2(1)3, with unit-cell parameters a = b = c = 203.0 A
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60
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pH 8.5, 0.75 M Tris-HCl, anaerobic condition, stable for 15 min
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
formate dehydrogenase activity is lost when the enzyme is exposed to oxygen. This instability is enhanced in low ionic strength buffers, detergents, at temperatures above 0°C, and at pH greater than 7
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698681
formate dehydrogenase is extremely sensitive to inactivation by oxygen in the presence of formate. Purified formate dehydrogenase is completely inactivated by aerobic incubation in 75 mM sodium phosphate, pH 7, for 1 h at 20°C in the presence of 50 mM formate, while only 40% of the activity is lost when the same incubation is carried out in the absence of formate. No activity is lost when the same incubation is carried out anaerobically even in the presence of formate
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698681
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE