Functional properties of the alternative NADH:ubiquinone oxidoreductase from E. coli through comparative 3‐D modelling

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Abstract
The alternative NADH:ubiquinone oxidoreductase (NDH‐2) from Escherichia coli is a membrane protein playing a prominent role in respiration by linking the reduction of NADH to the quinone pool. Remote sequence similarity reveals an evolutionary relation between alternative NADH:quinone oxidoreductases and the SCOP‐family “FAD/NAD‐linked reductases”. We have created a structural model for NDH‐2 from E. coli through comparative modelling onto a template from this family. Combined analysis of our model and sequence conservation allowed us to include the cofactor FAD and the substrate NADH in atomic detail. Furthermore, we propose the most plausible orientation of NDH‐2 relative to the membrane and specify a region of the protein potentially involved in ubiquinone binding.