CYTOCHROME c OX IDASE 437
bring the residue ’ s side chain in contact with the intermembrane surface. The
hydrogen - bonding network continues through the side - chain hydroxyl groups
of ser205 and ser441 and the backbone nitrogen of tyr440, and then it contin-
ues through a fi xed water molecule (H 2 O 5 ) in PDB: 1V54 and 1V55) to the
hydroxyl group of tyr371. Water molecule (H 2 O 5 ) also hydrogen - bonds to the
propionate group attached to pyrrole ring A of heme a. A second fi xed water
molecule connects tyr371 and arg38, with arg38 also hydrogen - bonded to
heme a ’ s formyl substituent. See Figure 7.41A , where some of the hydrogen -
bonding network is shown as red lines. The reference 142 authors postulate a
new model for the proton pumping process that is driven by a p Ka change in
asp51, involvement of heme a ’ s formyl group, and unidirectional proton trans-
fer through peptide bonds as well as water molecules. The hydrogen - bonding
network between arg38 and asp51 includes a peptide bond between tyr440
and ser441. The reference 142 authors summarize the overall process, called
the H pathway, in the following manner. For the oxidized state (PDB: 1V54),
(1) heme a contains the Fe(III) ion and carries a positive charge, (2) arg38
remains protonated (matrix water molecules are available to arg38 via a water
channel), and (3) asp51 is protonated and inside the protein membrane. Upon
reduction (PDB: 1V55), the following takes place: (1) The net positive charge
on heme a is removed because it now carries a Fe(II) ion, (2) asp51 is exposed
to the intermembrane space and its proton is released into this space, and (3)
the capacity of the water channel increases so that water molecules are taken
up from the matrix space. Upon heme oxidation, (1) asp51 moves back into
the protein ’ s interior, (2) the heme a ’ s positive charge decreases the affi nity
of the heme ’ s formyl group for the proton shared with arg38, (3) the decreased
proton affi nity promotes proton transfer from arg38 back to asp51, (4) depro-
tonated arg38 extracts a proton from a water molecule in the water channel,
and (5) a hydroxide ion is quickly released, preventing reverse proton transfer
(see Figure 2 and 4 of reference 142 ).
Published reports on electron transfer in cytochrome c oxidase usually
couple electron transfer with proton translocation. Several models have been
put forward that couple oxidation/reduction of the iron ion in heme a with
protonation/deprotonation of a proton pumping site. In a minireview pub-
lished inFEBS Letters in 2004, Namslauer and Brzezinski summarized the
structural elements involved in electron transfer as coupled to proton trans-
location in cytochrome c oxidase.^143 These authors described pathways postu-
lated for the bacteriumRhodobacter sphaeroides as determined from the
X - ray crystallographic structure of wild - type (PDB: 1M56) as well as an E286Q
(glu286gln) mutant (PDB: 1M57).^144 Two proton transfer pathways from the
matrix are identifi ed: (1) the D - pathway, named after an aspartic acid residue
in subunit I (asp132, D132), and (2) the K - pathway, named after the subunit
I residue lys362 (K362). PDB: 1M56, 1M57 numbering system is used in this
description. Note that it differs from that of PDB: 1V54, 1V55 discussed above.
The K - pathway may be used during reduction at the heme a 3 – Cu B catalytic
site, perhaps prior to the binding of dioxygen.