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Literature summary extracted from

  • Jormakka, M.; Toernroth, S.; Byrne, B.; Iwata, S.
    Molecular basis of proton motive force generation: structure of formate dehydrogenase-N (2002), Science, 295, 1863-1868.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.17.5.3 crystal structure at 1.6 A Escherichia coli

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.17.5.3 membrane alpha and beta subunits of Fdh-N are on the periplasmic side of the membrane Escherichia coli 16020
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Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.17.5.3 Fe 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 Escherichia coli

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.17.5.3 formate + menaquinone Escherichia coli 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 CO2 + menaquinol
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 ?

Organism

EC Number Organism UniProt Comment Textmining
1.17.5.3 Escherichia coli P24183 and P0AAJ3 and P0AEK7 P24183: subunit alpha, P0AAJ3: subunit beta, P0AEK7: subunit gamma
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Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.17.5.3 formate + menaquinone
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 Escherichia coli CO2 + menaquinol
-
 ?
1.17.5.3 formate + menaquinone 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 Escherichia coli CO2 + menaquinol
-
 ?

Subunits

EC Number Subunits Comment Organism
1.17.5.3 trimer alpha and beta subunits of Fdh-N are on the periplasmic side of the membrane Escherichia coli

Synonyms

EC Number Synonyms Comment Organism
1.17.5.3 Fdn-N
-
 Escherichia coli
1.17.5.3 formate dehydrogenase-N
-
 Escherichia coli
1.17.5.3 nitrate inducible Fdn
-
 Escherichia coli
1.17.5.3 nitrate inducible formate dehydrogenase
-
 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
1.17.5.3 bis(molybdopterin guanine dinucleotide)molybdenum cofactor 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 Escherichia coli
1.17.5.3 heme b 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 Escherichia coli
1.17.5.3 menaquinone 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 Escherichia coli