Bossis, Fabrizio; De Grassi, Anna; Palese, Luigi Leonardo; Pierri, Ciro Leonardo
Prediction of high- and low-affinity quinol-analogue-binding sites in the aa(3) and bo(3) terminal oxidases from Bacillus subtilis and Escherichia coli
BIOCHEMICAL JOURNAL, 461:305-314, JUL 15 2014

Haem-copper oxidases are the terminal enzymes in both prokaryotic and eukaryotic respiratory chains. They catalyse the reduction of dioxygen to water and convert redox energy into a transmembrane electrochemical proton gradient during their catalytic activity. Haem-copper oxidases show substantial structure similarity, but spectroscopic and biochemical analyses indicate that these enzymes contain diverse prosthetic groups and use different substrates (i.e. cytochrome c or quinol). Owing to difficulties in membrane protein crystallization, there are no definitive structural data about the quinol oxidase physiological substrate-binding site(s). In the present paper, we propose an atomic structure model for the menaquinol:O-2 oxidoreductase of Bacillus subtilis (QOx.aa(3)). Furthermore, a multistep computational approach is used to predict residues involved in the menaquinol/menaquinone binding within B. subtilis QOx.aa(3) as well as those involved in quinol/quinone binding within Escherichia coli QOx.bo(3). Two specific sequence motifs, R(70)GGXDX(4)RXQX(3)PX(3)FX[D/N/E/Q]X2HYNE97 and G(159)GSPX(2)GWX(2)Y(169) (B. subtilis numbering), were highlighted within QOx from Bacillales. Specific residues within the first and the second sequence motif participate in the high- and low-affinity substrate-binding sites respectively. Using comparative analysis, two analogous motifs, R(7)GFXDX(4)RXQX(8)[Y/F]XPPHHYDQ(101) and G(163)EFX(3)GWX(2)Y(173) (E. coli numbering) were proposed to be involved in Enterobacteriales/Rhodobacterales/Rhodospirillales QOx high- and low-affinity quinol-derivative-binding sites. Results and models are discussed in the context of the literature.

DOI:10.1042/BJ20140082

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