The flavodiiron proteins (FDP) are widespread among strict or facultative anaerobic prokaryotes, where they are involved in the response to nitrosative and/or oxidative stress. Unexpectedly, FDPs were fairly recently identified in a restricted group of microaerobic protozoa, including Giardia intestinalis, the causative agent of the human infectious disease giardiasis. The FDP from Giardia was expressed, purified, and extensively characterized by x-ray crystallography, stopped-flow spectroscopy, respirometry, and NO amperometry. Contrary to flavorubredoxin, the FDP from Escherichia coli, the enzyme from Giardia has high O 2 -reductase activity (>40 s ؊1 ), but very low NO-reductase activity (ϳ0.2 s ؊1 ); O 2 reacts with the reduced protein quite rapidly (milliseconds) and with high affinity (K m < 2 M), producing H 2 O. The three-dimensional structure of the oxidized protein determined at 1.9 Å resolution shows remarkable similarities with prokaryotic FDPs. Consistent with HPLC analysis, the enzyme is a dimer of dimers with FMN and the nonheme di-iron site topologically close at the monomer-monomer interface. Unlike the FDP from Desulfovibrio gigas, the residue His-90 is a ligand of the di-iron site, in contrast with the proposal that ligation of this histidine is crucial for a preferential specificity for NO. We propose that in G. intestinalis the primary function of FDP is to efficiently scavenge O 2 , allowing this microaerobic parasite to survive in the human small intestine, thus promoting its pathogenicity.The flavodiiron proteins (FDP, 2 originally named A-type flavoproteins (1)) are widespread among Bacteria and Archaea, either strict or facultative anaerobes, where they have been proposed to play a role in the response to nitrosative and/or oxidative stress (2, 3). A few prokaryotic FDPs have been characterized to date, namely those from the bacteria Desulfovibrio gigas (originally named rubredoxin:oxygen oxidoreductase, ROO (4 -7), and hereafter denoted FDP Dg ), Escherichia coli (named flavorubredoxin, FlRd, 3 Refs. 2, 8 -11), Desulfovibrio vulgaris (12), Moorella thermoacetica (FDP Mt , (13, 14)), and the homologous enzyme from the methanogenic archaeon Methanothermobacter marburgensis (FDP Mm , Refs. 15, 16). The FDPs contain two redox centers: a FMN, the electron entry site into the enzyme, and a non-heme Fe-Fe center, the active site (13). They are cyanide-insensitive enzymes able to catalyze the reduction of O 2 (to H 2 O) and/or NO (to N 2 O). Some of these enzymes are almost exclusively reactive toward NO (such as E. coli FlRd, Refs. 2, 9), 4 others toward O 2 (such as the M. marburgensis enzyme, (15)), whereas some FDPs catalyze the reduction of both gases, though with different efficiency (7,12,13). These enzymes are expected to play a protective role in anaerobic or microaerobic microorganisms that need to survive under O 2 and cope with NO produced by the host defense system to counteract infection (17,18).Surprisingly, a few years ago, genes coding for FDPs were identified also in the geno...