Discussion and Conclusions

Several membrane proteins that utilize quinone substrates have been crystallized and their structures determined without the bound quinone or bound with quinone analogues [9-11]. The initially reported structure of E. coli cyt bo3 does not have any

ubiquinol bound to the enzyme, but the subsequent structure determined by the Stowell group, using a different detergent, as part of our collaboration does have two long chain quinones bound. Most of the protein can be accounted for in the current structure, a substantial improvement over the previous structure [1]. Portions of the protein are clearly not in the native conformation (e.g., protein helices pointing perpendicular to the rest of the protein) when compared to the structures of homologous cytochrome c

oxidases [1, 12, 13]. and the overall resolution (3.8 Å) is still far from desired. Nevertheless, the data have been modeled to indicate a bound ubiquinone-8 with the headgroup where it is expected in the QH site and additional ubiquinone-8 bound opposite

side of the membrane. The ubiquinone at the QH site has most of the isoprene tail units

outside the protein, sticking out into what would be the lipid bilayer in the native environment. If representative of what is found in the membrane, this suggests that the head group and first few isoprene units (our of 8) are responsible for the binding affinity of ubiquinol-8.

Site-directed mutagenesis was performed based upon the new structure to observe the QL binding site functionality. The data clearly do not support the identification of this

as corresponding to the QL low affinity ubiquinol binding site. The KM was measured for

WT cyt bo3 to be 50 µM, which is the same as previously reported [2, 3, 14]. The KM of

the mutants showed essentially no change and, moreover, the activity of the mutants were also similar to the WT. Furthermore, our collaborators determined that the distance between the headgroups of the bound quinones at the QH and QL sites is substantially too

large (37 Å) to be compatible with the experimental electron transfer rate from QL to QH

[15-17]. A plausible explanation is that what has been modeled as a ubiquinone at the QL

site is actually a phospholipid or detergent. This is suggested by the fact that in the structure of the homologous cytochrome c oxidase from Rhodobacter sphaeroides (resolution of 2.3 Å, 1M56.pdb) there is a well defined lipid site that overlaps well with the putative QL site of cyt bo3. (Fig 3.3) We suggest this binding site is more likely to be

Overall, the essence of this part of our study is that the new structure helps with filling in the missing residues and moreover shows a natural substrate bound to the enzyme at the QH site. However, we still have not been able to identify the low affinity

ubiquinone binding site. The advantage of having a second ubiquinone binding site is to function as a transiently bound ubiquinone that is able to deliver electrons to the bound ubiquinone at the QH site. Therefore, the second ubiquinone binding site should be very

close to the QH site. It is not necessary for the ubiquinone to bind tightly to the second

site or to stabilize the semiubiquinone form in order to deliver two electrons to the bound ubiquinone at the QH site [2, 18].

Fig. 3.3 Structural comparison of top view between (left) cytochrome aa3 from

Rhodobacter sphaeroides (IM56.pdb) and (right) cytochrome bo3 from E.coli. First

ubiquinone (yellow) is well bound in the area known for the high affinity site (QH). In

cytochrome aa3 the lipid is bound at the same site where in cyt bo3, ubiquinone is bound.

The color is coded by the subunits. (black as subunit I, red as subunit II, pink as subunit III, and blue as subunit IV)

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