438 IRON-CONTAINING PROTEINS AND ENZYMES
In the D - pathway, water molecules and amino acid residues form a
hydrogen - bonding network that carries protons forward to a conserved glu-
tamic acid residue in subunit I (glu286, E286) where branching occurs. Some
protons are carried from this point toward the O 2 catalytic reduction site — the
substrate protons. Other protons, the pumped protons, are transferred toward
the cytosolic side (intermembrane space), perhaps via one of the histidines
ligated to Cu B^145 or one of the D - ring propionates of heme a or heme a 3.^146
Figure 1 of reference 144 and Figure 7.41B illustrate the pathways. In Figure
7.41B , water molecules are shown as red spheres, copper ions are shown as
copper colored space - fi ll spheres, the magnesium ion is shown as a green
space - fi ll sphere, and hemes and heme iron ions in stick format. D - and K -
pathway entrance amino acid residues are shown in green stick format. Hydro-
gen bonding network amino acid residues are visualized as blue sticks. All
amino acids are from subunit I, except E101 from subunit II. Red dashed lines
describe postulated proton translocation routes from matrix (bottom) to heme
a 3 – Cu B O 2 reduction site and exit pathways to the intermembrane space
(top).
When the wild - type structure (PDB: 1M56) was compared to the E286Q
mutant structure (PDB: 1M57), Iwata and co - workers^144 found structural rear-
rangements around the mutant site that could explain why the E286Q mutant
does not transfer protons. First, a hydrogen bond between glu286 and met107
cannot form. Second, structural changes around arg481 and arg482 are observed
that alter the interactions of these arg residues with the D - ring propionate of
heme a 3 (the arg481 – D - ring propionate salt bridge is broken resulting in an
increased p Ka for the propionate). Thus it appears likely that protonation or
deprotonation of glu286 is important, and is linked both to turnover at the
catalytic site and to the “ pumped protons ” pathway.
Several other models have been put forward that couple oxidation/reduc-
tion of the iron ion in heme a with protonation/deprotonation of a proton
pumping site.^147 One model proposed that the redox state of heme a controls
the position of water molecules connecting glu286, the D - ring propionate of
heme a 3 , and the catalytic site, thus providing a method of proton gating.^148 All
models propose that electron transfer (eT) is controlled by proton transfer
(pT). For instance, heme a ’ s role may be to control the timing of eT from
cytochrome c/Cu A to the catalytic site so that eT is prevented until the key
residue, glu286, is reprotonated.
Figures 7.42 and 7.40 illustrate two schemes describing proton translocation
and electron transfer within cytochrome c oxidase. Figure 7.42 illustrates the
cycle beginning with fully reduced enzyme — that is, CuAI−CuAI, with both
hemes carrying Fe II ions and CuBI. Figure 7.40 begins the cycle in a so - called
mixed valence state — that is, CuAI−CuAII, with heme a carrying an Fe III ion and
heme a 3 carrying an Fe II ion and CuBI (changes from the fully reduced form
in bold). Similar schemes are found in references 138 , 140 , and 143. The refer-
ence 140 authors describe both fully reduced and mixed valence possibilities
in their Figure 11.