The ability to reduce nitrate (NO3^-) to ammonia (NH3) is common to virtually all plants, fungi, and bacteria. It occurs in the following four steps:

NO3^- -> NO2^- -> NO^- -> NH2OH -> NH3.

The first step, conversion of NO3^- to NO2^-, is catalyzed by a large and complex enzyme called nitrate reductase. Nitrate reductase is a multi-subunit enzyme with Mr of about 800 kD. It contains bound FAD, molybdenum, and a cytochrome called cytochrome 557 (which contains an Fe4S4 complex). Nitrate reductase carries out the following reaction:

NO3^- + NAD(P)H + H⁺  -> NO2^- +  NADP⁺ + H2O

Plants use NADH. Fungi and bacteria use NADPH. The molybdenum is bound to a cofactor containing a pteridine ring to form molybdopterin (see here). All molybdenum-requiring enzymes except nitrogenase contain a structure similar to molydopterin.

Another interesting molybdenum-containing enzyme is dimethylsulfoxide reductase (Figure 20.6). It contains two molecules of bound molybdopterin covalently linked to a serine residue in the enzyme.

The last three steps in the reduction of nitrate to ammonia are carried out by an enzyme called nitrite reductase. It contains one Fe2S2 center and one molecule of siroheme, a partially reduced iron porphyrin. The electron donor for each step is ferredoxin.