Ubiquinone binding sites

Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S. 2000. The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. Nat Struct Biol 7 910. 

Unlike the other ubiquinol binding sites presented above, the ubiquinol binding site in cytochrome bo% stabilizes a semiquinone during the oxidation of ubiquinol. A previous model placed the ubiquinone binding site of cytochrome bo within the extrinsic domain of subunit II, replacing the Cua site (Murray et al., 1999). However, several lines of evidence are available to refute this model. 

To begin with, the proposed ubiquinone binding site was unlike any of the previous sites that have been described in membrane proteins that bind ubiquinone. As presented above the photosynthetic reaction center (Deisenhofer etal., 1995), the bc complex (Xia etal., 1987 Zhang et al., 1998 Iwata et al., 1998 Hunte et al., 2000), and fumarate reductase (Iverson et al., 1999 Lancaster et al., 1999) bind the ubiquinone molecule within membrane-spanning helices where the ring of the ubiquinone molecule is oriented near the phospholipid head group of the membrane. Second, a large mutational study of residues at or around... 

In the h positional state , tiie distance is > 30 A between the Rieske cluster and cytochrome Cl whereas in the ci positional state , tiie Rieske [2Fe-2S] cluster is far away from tiie ubiquinone binding site and points in tiie opposite direction (Figure 3). Therefore, tiie Rieske protein has to move between these positional states in order to transfer an electron fiom ubihydroquinone to cytochrome Ci. The movement involves a rotation of the entire water soluble domain of 57 this rotation requires stretching of the flexible linker. 

Figure 6. Amino acid side chains near the secondary ubiquinone binding site in the light adapted structure (green) of the Rb. sphaeroides RC. One oxygen of ubiquinone is within hydrogen bonding distance of the His LI 90 side chain and the Glu L212 side chain is oriented further away. Also shown is the binding site of UQb in the dark adapted structure (blue) and the Phe L216 side chain (Createdfrom coordinates reported in reference 14. Isoprenyl chains of the ubiquinones have been truncated for clarity).

Complex II, succinate-ubiquinone oxido-reductase. Complex II, which carries electrons from succinate to ubiquinone, contains covalently linked 8 -(Af-histidyl)-FAD (Chapter 15) as well as Fe-S centers and one or more ubiquinone-binding sites. There are four subunits whose structures and properties have been highly conserved among mitochondria and bacteria and also in fumarate reductases. The latter function in the opposite direction during anaerobic respiration with fumarate as the terminal oxidant, both in bacteria and in parasitic helminths and other eukaryotes that can survive prolonged anaerobic conditions (Chapter 17, Section F,2). °° Complex II from E. coli consists of 64-, 27-, 14-, and 13-kDa subunits, which are encoded by genes sdhCDAB of a single... 

S. Iwata, and M. Wikstrom, The Structure of the Ubiquinol Oxidase from E. coli and its Ubiquinone Binding Site. Nature Struct. Biol., 7, 910-917,2000. 

ALS shows a high degree of primary sequence homology with pyruvate carboxylase and pyruvate oxidase the ubiquinone cofactors of pyruvate oxidase inhibit ALS, and it has been proposed that the ubiquinone-binding site of the ancestral enzyme also is the site of both SMM and imidazolinone binding. Recent evidence suggests, however, that these two types of herbicide interact differently with ALS (a) imidazolinones cause a rapid decrease in the levels of extractable ALS activity in maize, whereas SMM does not and can protect the ALS activity from this in vivo effect of imidazolinones and (b) not all imidazolinone-tolerant cell lines are insensitive to sulfonylureas. Sulfonylureas and imidazolinones do not, however, show synergistic inhibition of maize ALS in vitro. ... 

---