Structural Basis for the Quinone Reduction in thebc₁Complex:  A Comparative Analysis of Crystal Structures of Mitochondrial Cytochromebc₁with Bound Substrate and Inhibitors at the Q_iSite^,

Abstract

Cytochrome bc(1) is an integral membrane protein complex essential to cellular respiration and photosynthesis. The Q cycle reaction mechanism of bc(1) postulates a separated quinone reduction (Q(i)) and quinol oxidation (Q(o)) site. In a complete catalytic cycle, a quinone molecule at the Q(i) site receives two electrons from the b(H) heme and two protons from the negative side of the membrane; this process is specifically inhibited by antimycin A and NQNO. The structures of bovine mitochondrial bc(1) in the presence or absence of bound substrate ubiquinone and with either the bound antimycin A(1) or NQNO were determined and refined. A ubiquinone with its first two isoprenoid repeats and an antimycin A(1) were identified in the Q(i) pocket of the substrate and inhibitor bound structures, respectively; the NQNO, on the other hand, was identified in both Q(i) and Q(o) pockets in the inhibitor complex. The two inhibitors occupied different portions of the Q(i) pocket and competed with substrate for binding. In the Q(o) pocket, the NQNO behaves similarly to stigmatellin, inducing an iron-sulfur protein conformational arrest. Extensive binding interactions and conformational adjustments of residues lining the Q(i) pocket provide a structural basis for the high affinity binding of antimycin A and for phenotypes of inhibitor resistance. A two-water-mediated ubiquinone protonation mechanism is proposed involving three Q(i) site residues His(201), Lys(227), and Asp(228).

Resolving the EPR Spectra in the Cytochrome bc 1 Complex from Saccharomyces cerevisiae

“…Each of the two latter residues is in a position for direct hydrogen bonding with one of the quinone carbonyl oxygen atoms, suggesting a direct proton transfer. However, in contrast, Xia's [8] group described for the structure of the bovine complex that both the histidine and aspartate hydrogen bonds are mediated by water molecules.…”

X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc1: Comparison with its Mitochondrial and Chloroplast Counterparts

“…Indeed, a great deal of information is available concerning the effects of single, as well as compensatory pairs of point mutations on the assembly and function of Rhodobacter cyt bc 1 (Brasseur et al 1996). While the interpretation of these data has been greatly aided by the availability of the mitochondrial structures (Xia et al 1997;Iwata et al 1998;Zhang et al 1998;Hunte et al 2000;Gao et al 2003;Palsdottir et al 2003), there are also important differences due to specific insertions and deletions that are uniquely present in the bacterial or mitochondrial enzymes.…”

“…Various three dimensional structures of the mitochondrial cyt bc 1 , which have been accumulated during the last several years (Xia et al 1997;Iwata et al 1998;Zhang et al 1998;Hunte et al 2000;Gao et al 2003;Palsdottir et al 2003), have recently been supplemented by the structures of the cyt b 6 f from cyanobacteria and chloroplast (Kurisu et al 2003;Stroebel et al 2003). Crystallization of the simpler bacterial cyt bc 1 has been 6 considerably more challenging, and the crystals obtained to date are not particularly satisfactory for structure determination due to high mosaicity as well as poor and anisotropic crystalline order.…”

Antimalarial 4(1H)-pyridones bind to the Q i site of cytochrome bc 1

“…The Q i site of cytochrome bc 1 has been far less explored in the search for antimalarial compounds and only the binding of a few compounds has been visualized directly (38)(39)(40). Several compounds have been suggested to bind the Q i site, including potential antimalarial compounds, but due to lack of structural information have not been pursued vigorously (41).…”