We have used site-directed mutagenesis, EPR spectroscopy, redox potentiometry, and protein crystallography to monitor assembly of the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor (Mo-bisPGD) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). Cys and Ser mutants of NarG-His 49 both lack catalytic activity, with only the former assembling FS0 and Mo-bisPGD. Importantly, both prosthetic groups are absent in the NarG-H49S mutant. EPR spectroscopy of the Cys mutant reveals that the E m value of the FS0 cluster is decreased by at least 500 mV, preventing its participation in electron transfer to the MobisPGD cofactor. To demonstrate that decreasing the FS0 cluster E m results in decreased enzyme activity, we mutated a critical Arg residue (NarG-Arg 94 ) in the vicinity of FS0 to a Ser residue. In this case, the E m of FS0 is decreased by 115 mV, with a concomitant decrease in enzyme turnover to ϳ30% of the wild type. Analysis of the structure of the NarG-H49S mutant reveals two important aspects of NarGHI maturation: (i) apomolybdoNarGHI is able to bind GDP moieties at their respective P and Q sites in the absence of the Mo-bisPGD cofactor, and (ii) a critical segment of residues in NarG, 49 HGVNCTG 55 , must be correctly positioned to ensure holoenzyme maturation.Escherichia coli, when grown anaerobically with nitrate as respiratory oxidant, develops a respiratory chain terminated by a membrane-bound quinol:nitrate oxidoreductase (NarGHI) (1-3). This enzyme is an archetype of the complex iron-sulfur molybdoenzyme (CISM) 2 family (4) that includes E. coli formate dehydrogenase N (FdnGHI (5)), E. coli Me 2 SO reductase (DmsABC (6)), Wolinella succinogenes polysulfide reductase (PsrABC (7, 8)), Salmonella typhymurium thiosulfate reductase (PhsABC (9)), and Salmonella enterica tetrathionate reductase (TtrABC (10)). These enzymes and their close relatives contribute significantly to the remarkable metabolic diversity of bacteria.NarGHI and the other CISM archetypes comprise a mononuclear molybdenum cofactor (molybdo-bis(pyranopterin guanine dinucleotide) (Mo-bisPGD))-containing catalytic subunit, e.g. NarG; a four-cluster protein subunit, e.g. NarH; and a membrane anchor protein, e.g. NarI. Each catalytic subunit contains a [4Fe-4S] cluster in addition to MobisPGD, and many of the membrane anchor subunits are also diheme cytochromes b. The five [Fe-S] clusters are referred to as FS0 -FS4, with increasing distance from Mo-bisPGD, and the entire electron transfer relay (ETR) in NarGHI, including the two hemes, spans a distance of almost 100 Å (2).In NarGHI, Mo-bisPGD provides the site of nitrate reduction at its redox-active molybdenum atom. The molybdenum atom is coordinated by two pyranopterin guanine dinucleotide (PGD) moieties via a bis-dithiolene linkage (11-13). These PGD groups are referred to as the P-and Q-pterins, and they are proximal and distal, respectively, to the FS0 [4Fe-4S] cluster. The bis-dithiolene coordination is supplemented by one oxo gr...