390 IRON-CONTAINING PROTEINS AND ENZYMES
cytochrome c 1. On the intermembrane side, cytochrome c 1 , the ISP, and subunit
8 sit on top of cytochrome b. Subunits 10 and 11 maintain contact between
cytochrome c 1 and the ISP and may assist in forming the bc 1 complex. Subunit
9 is the mitochondrial targeting presequence of the ISP. This means that in
eukaryotes the ISP is nuclear - coded and posttranslationally imported into the
mitochondria and then inserted into the inner membrane. In PDB: 1BE3 and
PDB: 1BGY, subunit 9 is found between the core 1 and core 2 subunits. These
large subunits may be MPPs (mitochondrial processing peptidases), proteins
that cleave targeting presequences after they are imported into the mitochon-
dria. In the dimer, as with cytochrome b(6)f, the ISP from one monomer
interacts with cytochromes b and c 1 of the other monomer. Electron transfer
can only take place when the dimer is assembled; otherwise the electron -
carrying hemes and [2Fe – 2S] centers are too far apart.
By the end of 1998, fi ve X - ray crystallographic structures of the cytochrome
bc 1 complex had been published: (1) PDB: 1QCR, reference 79 ; (2) PDB:
1BE3, 1BGY, reference 83 ; and (3) PDB: 1BCC, 3BCC, reference 84. These
snapshots along cytochrome bc 1 ’ s dynamic pathway of electron transfer and
proton translocation gave researchers insight not only into the enzyme ’ s struc-
ture but also into its mechanism of activity. One of the important fi ndings
was the changing position of the iron – sulfur protein (ISP) with its [2Fe – 2S]
center — it moves as much as 20 Å and rotates as much as 60 °. As the data to
be presented will show, the ISP appears to change from positions close to
cytochrome c 1 to positions close to heme b L within cytochrome b while the
positions of heme b L and b H remain fi xed with respect to each other and the
membrane bilayer. As stated in Section 7.6.1 , these structures also indicated
that dimer formation was essential for electron transfer and proton transloca-
tion to take place in cytochrome bc 1 complex. The enzyme complex contains
a cavity between the two monomers of the essential dimer that were thought
to allow passage of substrate ubiquinol/ubiquinone to and from the complex
and between two active sites for oxidation and/or reduction, Q N (Q o in most
publications) and Q P (Q i in most publications). An informative cartoon illus-
trating the complete dimer is found in the perspective by J. L. Smith accom-
panying theScience magazine publication, reference 83.^85
In 1998, B. K. Jap, S. Iwata, and co - workers solved the complete structure
of the 11 - subunit mitochondrial cytochrome bc 1 complex using X - ray crystal-
lography of two different crystalline forms, both of which were obtained from
oxidized bovine heart mitochondrial bc 1 complex (PDB: 1BE3 equals the
P6 5 22 form and 1BGY equals the P6 5 form).^83 The asymmetric unit of the P6 5 22
form, refracting to a resolution of 3.0 Å , contains one monomer of 11 subunits
related to the other monomer of the dimer by a crystallographic twofold sym-
metry axis. The P6 5 form (PDB: 1BGY), refracting to 2.8 - Å resolution, con-
tains the whole dimer. The P6 5 22 form ’ s R factor (28.5%) is high compared to
ordinary water - soluble proteins due to partially ordered co - crystallized lipids
not accounted for in the model. In the two different crystal forms, the ISP
domains are found in different positions as has been reported for other bovine