404 IRON-CONTAINING PROTEINS AND ENZYMES
inhibitor NQNO (PDB: 1NUI) competes with ubiquinone for the Q i pocket
and binds in the Q o pocket as well (a Xia classifi cation PN inhibitor). This
structure will not be discussed further.
It was known from previous research that the inhibitors antimycin A and
NQNO (2 - nonyl - 4 - hydroxyquinoline N - oxide) specifi cally inhibit activity at
the Q i site (the quinone reduction site) where a quinone molecule receives
two electrons from heme b H and two protons from the negative side of the
membrane. Antimycin A was one of the fi rst known and is still one of the most
potent inhibitors of the mitochondrial respiratory chain. The antimycin A 1
molecule (see Figure 7.29 ) consists of three parts: (1) a nine - member puckered
dilactone ring in the center; (2) a 3 - formylamino salicylic acid (3 - FASA) group
connected to the dilactone through an amide bond; and (3) a hydrophobic tail
on the other side of the dilactone ring. The dilactone ring consists of an l -
threonine (connected to the salicylate through the amide bond) and a 2 - alkyl -
3,4 - dihydroxyvalerate. It is believed that the 3 - FASA portion of the molecule
is responsible for the binding specifi city. In the antimycin A molecule itself, an
intramolecular hydrogen bond exists between the hydroxy group on the 3 -
FASA aromatic ring and the carbonyl oxygen group of the amide bridge. This
hydrogen bond is illustrated in Figure 7.29 for the antimycin A molecule with
the PDB: 1NTK label. As we will see later, the numbering system (and the
intramolecular hydrogen bond) is different for antimycin A in the PDB: 1PPJ
structure to be discussed next. Antimycin A 1 binds in the Q i pocket and is
therefore called a class II inhibitor or, in the nomenclature of Xia et al., an N
inhibitor. Antimycin A 1 binds through a network of six hydrogen bonds and
one Ar – Ar interaction. The 3 - FASA N 1 atom hydrogen bonds to O δ 1 of asp228
(N 1 · · · O δ 1 = 3.0 Å ), while the O δ 2 of asp228 binds to the 3 - FASA hydroxyl
oxygen (O 2 · · · O δ 2 = 2.3 Å ). Atom O γ (OH) of ser35 interacts with dilactone car-
bonyl group O 7 (O 7 · · · O γ = 3.7) and the carbonyl group with oxygen O 3 , in the
amide linker (O 3 · · · O γ = 3.0). The N ε 2 atom of his201 and the carbonyl oxygen
of ala17 hydrogen bond through two water molecules (2.8 Å apart) to the
antimycin A N 2 salicyamide group. The aromatic group of phe220 has an edge -
to - face distance to the 3 - FASA ring of 3.1 Å , forming an Ar – Ar interaction.
The hydrogen - bonding amino acid residues are part of the Q i cavity formed
by residues from transmembrane helices A (trp31, asn32, gly34, ser35), D
(ala193, met194, leu197, his201), and E (tyr224, lys227, asp228). Residues from
the amphipathic (having both negatively and positively charged — hydro-
philic — as well as hydrophobic aa residues) surface helix A (phe18), from the
A loop (ile27), and from the DE loop (ser205, phe220), and atoms from the
high potential heme b H (carbon atoms and a propionate side chain) also line
the Q i cavity.
In 2005, the E. A. Berry group published X - ray crystallographic studies of
cytochrome bc 1 with bound inhibitors.^90 The structure of PDB: 1PP9, resolu-
tion 2.23 Å , includes stigmatellin A (SMA) in the Q o site and substrate ubi-
quinone (UQ) in the Q i site, while PDB: 1PPJ, resolution 2.28 Å , includes
stigmatellin A in the Q o site and antimycin A 1 (ANY) in the Q i site. These