CYTOCHROME bc 1 : A BACTERIAL CYTOCHROME 399
hydroxyl groups. The closest approach of a UQ2 atom is that of its methoxy
oxygen O 2 to the glu271 backbone N at a distance of 4.1 Å. An intervening
water molecule does bring these two atoms within hydrogen - bonding distance
(UQ2 O 2 · · · H 2 O 1069 = 2.8 Å , H 2 O 1069 · · · E271 N = 3.1 Å in PDB: 1NTZ). The
Nε 2 atom of his161 is 4.6 Å distant from the UQ2 carboxyl oxygen O 4. The
isoprenoid tail of UQ2 has hydrophobic contacts with phe274 in cytochrome
b ’ s EF loop (short helix ef) as well as met124, ala125, and met129 in the C
helix.
In the Q i pocket for the PDB: 1NTZ structure, ubiquinone - 2 binds in a dif-
ferent manner than the inhibitor antimycin A 1 (see discussion of antimycin A 1
inhibitors below). Different Q i amino acid residues interact with the substrate
substitute UQ2: (1) leu 200, his201, ser205, tyr224, lys227, and asp228 are
important in ubiquinone - 2 binding, and (2) trp31, gly38, met190, met194,
leu197, and ser35 provide specifi c interactions with antimycin A 1. In the Q i
pocket, hydrogen bonds are formed between a UQ2 carbonyl oxygen and an
asp228 side - chain oxygen (UQ2 O 1 · · · asp228 O δ 2 = 2.5 Å ), a second UQ2 car-
bonyl oxygen and a hydroxyl oxygen of ser205 (UQ2 O 4 · · · ser205 O γ = 4.0 Å ),
a UQ2 methoxy (OCH 3 ) oxygen with the hydroxyl oxygen of ser205 (UQ2
O 3 · · · ser205 O γ = 2.7 Å ), and an interaction between the N ε 2 nitrogen and a UQ2
carbonyl group mediated by a water molecule (UQ2 O 4 · · · H 2 O = 3.4 Å ,
H 2 O · · · his201 N ε 2 = 2.6 Å ). In addition, an edge - to - face phe220 – ubiquinone - 2
quinone ring Ar – Ar interaction, similar to that for antimycin A 1 , is evident.
The closest interaction distance between ubiquinone - 2 in the Q i site and the
heme b H is 4.2 Å.
Effects of the myxothiazol inhibitor on the cytochrome bc 1 complex were
studied by the Trumpower group beginning in 1984.^89 The researchers found
effects identical to those caused by removal of the iron – sulfur protein (ISP)
from the complex. Reduction of heme c 1 is blocked but not the reduction of
the b hemes, b L and b H. If the antibiotic antimycin A was present, reduction
of all cytochromes hemes was found. Myxothiazol also inhibits reduction of
the ISP by ubiquinol. These and other effects were found to be consistent with
the proton - motive Q - cycle pathway of electron transfer in which the myxo-
thiazol inhibitor binds to cytochrome b and displaces ubiquinol/ubiquinone
from the ISP and Q o site. The reference 89 authors postulated that (1) a myxo-
thiazol - induced conformational change in cytochrome b is transmitted to the
ubiquinone - binding site on the ISP, or (2) there is a ubiquinone - binding site
consisting of peptide domains from both cytochrome b and the ISP. Recent
X - ray crystallographic studies have shown postulate (2) to be correct, while
postulate (1) structural proofs remain elusive.
The Di Xia research group has completed X - ray crystallographic studies of
cytochrome bc 1 with a number of different inhibitors^88 (PDB: 1SQB, 1SQP,
1SQQ, 1SQV, 1SQX). Crystals suitable for crystallography were obtained by
co - crystallization of the inhibitor with the native enzyme. Data for two of
the inhibitor - modifi ed cytochrome bc 1 complex (PDB: 1SQP and 1SQX) are
included in Table 7.6 and Table 7.7. One inhibitor – enzyme complex studied by