The membrane-bound nitrate reductase-A (NR-A) (NarGHI; α₂β₂γ₄, β, and γ in E. coli; also called NR-1) employs a redox loop to couple quinol oxidation to the equivalent of proton translocation, thereby generating a proton motive force (pmf) during anaerobic respiration. In this process, ubiquinol oxidation by the cytochrome b subunit (NarI) occurs at the periplasmic side of the membrane, releasing two protons, and nitrate reduction by NarG occurs in the cytoplasm, consuming two protons to form water. There is therefore a net loss of H⁺ in the cytoplasm and a net gain of H⁺ in the periplasm with transmembrane electron flow from the periplasm to the cytoplasm, generating a pmf, negative inside (Rothery et al., 2007).

NarGHI contains Mo-molybdopterin guanine dinucleotide, FMN(H₂), selenocysteine, five iron-sulfur centers and diheme cytochrome b₅₅₆. The enzyme is strongly inhibited by azide (N₃^-). Synthesis is maximal during anaerobic growth in the presence of nitrate. The α-subunit (NarG; 1247 aas) is the site of NO₃^- reduction to NO₂^-. The molybdenum cofactor, selenocysteine, FMNH₂ and one iron-sulfur center are all present in NarG. The NarH (β) subunit (512 aas) contains four more iron sulfur centers. The NarI (γ) subunit (225 aas; 5 putative TMSs) is the integral membrane b-type cytochrome that anchors the α and β subunits to the membrane on the cytoplasmic side and oxidizes quinol on the periplasmic side (Jormakka et al., 2002; Rothery et al., 2007).

Like NR-A, formate dehydrogenase (FDH) is a three subunit enzyme (FdnGHI) homologous to nitrate reductase-A. It has an α₂β₂γ ₄ subunit composition and contains the same cofactors as does nitrate reductase. The dehydrogenase transfers an electron pair across the membrane from formate (in) to quinone (out). It probably uses the same mechanism as that described above for nitrate reductase.

The soluble α-subunits of NR-A and FDH are homologous to the α-subunits of other soluble molybdo-cofactor proteins such as DMSO reductase, TMAO reductase, biotin sulfoxide reductase and thiosulfate reductase. The soluble β-subunits of NR-A and FDH show some sequence similarity to subunit F of the tungstate-containing formyl methanofuran dehydrogenase of Methanobacterium thermoautotrophicum (TC #3.D.8.1.1). Additionally they are homologous to β-subunits of the oxidoreductases cited above plus selenate reductase, tetrathionate reductase, polysulfide reductase, hydrogenases, carbon monoxide reductase, ferridoxin, polyferridoxin, etc. The NarI (γ) subunit is more sequence divergent than the α or β subunits but is homologous to a subunit in the archaeal heterodisulfide reductase (TC #3.D.7). The FdnI (γ) subunit of FDH has 4 predicted TMSs in contrast to NarI which has 5. The NarJ protein (P11351, sometimes called the δ-subunit) is required for assembly of the NR-cytochrome b complex.

The net overall reaction catalyzed by NR-A is probably:

nitrate (NO₃^-) (in) + quinol (out) + 2H⁺ (in) → nitrite (NO₂^-) (in) + quinone (out)
+ 2H⁺ (out) + H₂0 (in).

The overall reaction catalyzed by formate dehydrogenase is probably:

formate (HCO₂^-) (in) + quinone (out) + 2H⁺ (out) → CO₂ (in) + quinol (out) + H⁺ (in).

The net transmembrane electron transfer reactions for NR-A and FDH, and probably other homologous enzymes are:

(a) 2e^- (out) → 2e^- (in) (NR-A)

(b) 2e^- (in) → 2e^- (out) (FDH)