Edited by Norma AllewellComplex III or the cytochrome (cyt) bc 1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc 1 is to couple the reaction of electron transfer from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the electron transfer reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation site (Q P ) of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking. Here we show that the binding of oxazolidinedione-type inhibitors famoxadone, jg144, and fenamidone induces docking of the ISP to the Q P site in the absence of the H-bond formation both in mitochondrial and bacterial cyt bc 1 complexes, demonstrating that ISP docking is independent of the proposed direct ISP-inhibitor interaction. The binding of oxazolidinedione-type inhibitors to cyt bc 1 of different species reveals a toxophore that appears to interact optimally with residues in the Q P site. The effect of modifications or additions to the toxophore on the binding to cyt bc 1 from different species could not be predicted from structure-based sequence alignments, as demonstrated by the altered binding mode of famoxadone to bacterial cyt bc 1 .The ubiquinol-cytochrome c oxidoreductase, also known as complex III of mitochondrial respiratory chain or cytochrome (cyt) 3 bc 1 complex, catalyzes the reaction of electron transfer (ET) from ubiquinol (QH 2 ) to cyt c and concomitantly translocates protons across the inner membrane of mitochondria or the plasma membrane of photosynthetic purple bacteria, contributing to a cross-membrane potential important for cellular function (1, 2). Although catalyzing the same enzymatic reaction, cyt bc 1 complexes isolated from different organisms have very different subunit compositions. Prokaryotic bc 1 complexes often consist of 3-4 subunits, whereas mitochondrial enzymes have 10 -11 different subunits (1). Nevertheless, only three subunits are essential for the ET function ( Fig. 1A): cyt b, cyt c 1 , and the Rieske iron-sulfur protein (ISP) (3). The cyt b subunit contains two b-type hemes, b L and b H , for the low and high potential hemes, respectively, and is entirely embedded in the membrane with eight transmembrane (TM) helices (4). The cyt c 1 subunit, anchored to the membrane by a single TM helix, has a c-type heme covalently attached to its active domain that is located in the intermembrane space of mitochondria or periplasm in bacteria. The ISP subunit features an integrated 2Fe-2S cluster in its extrinsic domain (ISP-ED) that is on the same side as the cyt c 1 subunit and also anchored to the membrane by a helix. The ET-coupled proton translocation function, as modeled by the Q-cycle mechanism (Fig. 1B), requires two active sites: a QH 2 oxidation (Q P ) site and a ubiquinone (Q) reduction (Q N ) site (5-7), which were shown to exist by crystal structu...