YLR011wp structure ribbon representation and FMN binding mode. a, ribbon representation of the YLR011wp monomer. Helices, strands, and loops are colored blue, pink, and orange, respectively. Insertions relative to the canonical flavodoxin fold are colored green (Insertion I) and red (Insertion II). Bound FMN is represented by sticks. b, stereoview of the FMN binding site with the hydrogen bonds indicated by dashed lines. The FMN phosphorus and the cysteine sulfur atoms are colored gray and green, respectively. For clarity, amino acid single letter code is used in every figure. c and d, stick representation of the FMN phosphate binding mode in YLR011wp (c) and in "classical" flavodoxins (d) (flavodoxin from A. nidulans is considered the classical flavodoxin prototype in our study (5)). For clarity, side chains not involved in hydrogen bonds have been omitted. Hydrogen bonds are depicted by dashed lines.

Flavodoxins are involved in a variety of electron transfer reactions that are essential for life. Although FMN-binding proteins are well characterized in prokaryotic organisms, information is scarce for eukaryotic flavodoxins. We describe the 2.0-Å resolution crystal structure of the Saccharomyces cerevisiae YLR011w gene product, a predicted flavoprotein. YLR011wp indeed adopts a flavodoxin fold, binds the FMN cofactor, and self-associates as a homodimer. Despite the absence of the flavodoxin key fingerprint motif involved in FMN binding, YLR011wp binds this cofactor in a manner very analogous to classical flavodoxins. YLR011wp closest structural homologue is the homodimeric Bacillus subtilis Yhda protein (25% sequence identity) whose homodimer perfectly superimposes onto the YLR011wp one. Yhda, whose function is not documented, has 53% sequence identity with the Bacillus sp. OY1-2 azoreductase. We show that YLR011wp has an NAD(P)H-dependent FMN reductase and a strong ferricyanide reductase activity. We further demonstrate a weak but specific reductive activity on azo dyes and nitrocompounds.