Formate dehydrogenases are a set of enzymes that catalyse the oxidation of formate to carbon dioxide, donating the electrons to a second substrate, such as NAD+ in formate:NAD+ oxidoreductase (EC1.17.1.9) or to a cytochrome in formate:ferricytochrome-b1 oxidoreductase (EC1.2.2.1).[1] This family of enzymes has attracted attention as inspiration or guidance on methods for the carbon dioxide fixation, relevant to global warming.[2]
Function
NAD-dependent formate dehydrogenases are important in methylotrophicyeast and bacteria, being vital in the catabolism of C1 compounds such as methanol.[3] The cytochrome-dependent enzymes are more important in anaerobic metabolism in prokaryotes.[4] For example, in E. coli, the formate:ferricytochrome-b1 oxidoreductase is an intrinsic membrane protein with two subunits and is involved in anaerobic nitrate respiration.[5][6]
The metal-dependent Fdh's feature Mo or W at their active sites. These active sites resemble the motif seen in DMSO reductase, with two molybdopterin cofactors bound to Mo/W in a bidentate fashion. The fifth and sixth ligands are sulfide and either cysteinate or selenocysteinate.[7]
The mechanism of action appears to involve 2e redox of the metal centers, induced by hydride transfer from formate and release of carbon dioxide:
S=MVI(Scys)(SR)4 + HCO−2 ⇌ HS−MIV(Scys)(SR)4 + CO2
S=MVI(Secys)(SR)4 + HCO−2 ⇌ HS−MIV(Secys)(SR)4 + CO2
In this scheme, (SR)4 represents the four thiolate-like ligands provided by the two dithiolene cofactors, the molybdopterins. The dithiolene and cysteinyl/selenocysteinyl ligands are redox-innocent. In terms of the molecular details, the mechanism remains uncertain, despite numerous investigations. Most mechanisms assume that formate does not coordinate to Mo/W, in contrast to typical Mo/W oxo-transferases (e.g., DMSO reductase). A popular mechanistic proposal entails transfer of H- from formate to the Mo/WVI=S group.[8]
Formate Dehydrogenase (PDB 1KQF, 1.6 A resolution, from E. coli); overall view of the electron transport chain showing the [Fe4S4] clusters in the periplasmic alpha and beta subunits, and the cytoplasmic gamma subunit showing the Fe(heme b)P and the Fe-(heme b)C menoquinone binding site where an HQNO ligand is bound close the Fe(heme b)C. Atom colours: Fe = orange, S = yellow, C = grey, O = red, N = blue.
Transmembrane domain
Formate dehydrogenase consists of two transmembrane domains; three α-helices of the β-subunit and four transmembrane helices from the gamma-subunit.
The β-subunit of formate dehydrogenase is present in the periplasm with a single transmembrane α-helix spanning the membrane by anchoring the β-subunit to the inner-membrane surface. The β-subunit has two subdomains, where each subdomain has two [4Fe-4S] ferredoxin clusters. The judicious alignment of the [4Fe-4S] clusters in a chain through the subunit have low separation distances, which allow rapid electron flow through [4Fe-4S]-1, [4Fe-4S]-4, [4Fe-4S]-2, and [4Fe-4S]-3 to the periplasmic heme b in the γ-subunit. The electron flow is then directed across the membrane to a cytoplasmic heme b in the γ-subunit .
The γ-subunit of formate dehydrogenase is a membrane-bound cytochrome b consisting of four transmembrane helices and two heme b groups which produce a four-helix bundle which aids in heme binding. The heme b cofactors bound to the gamma subunit allow for the hopping of electrons through the subunit. The transmembrane helices maintain both heme b groups, while only three provide the heme ligands thereby anchoring Fe-heme. The periplasmic heme b group accepts electrons from [4Fe-4S]-3 clusters of the β-subunit’s periplasmic domain. The cytoplasmic heme b group accepts electrons from the periplasmic heme b group, where electron flow is then directed towards the menaquinone (vitamin K) reduction site, present in the transmembrane domain of the gamma subunit. The menaquinone reduction site in the γ-subunit, accepts electrons through the binding of a histidine ligand of the cytoplasmic heme b.[9]
Menaquinone binding site alongside proposed water proton pathway
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