title: Structural basis for the quinone reduction in the bc1 complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1 with bound substrate and inhibitors at the Qi site.
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).
authors.affiliation: Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Xiugong
authors.initials: X
authors.lastname: Gao
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Wen
authors.forename: Lothar
authors.initials: L
authors.lastname: Esser
authors.forename: Byron
authors.initials: B
authors.lastname: Quinn
authors.forename: Linda
authors.initials: L
authors.lastname: Yu
authors.forename: Chang-An
authors.initials: CA
authors.lastname: Yu
authors.forename: Di
authors.initials: D
authors.lastname: Xia
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000968:Antimycin A / Q000737:chemistry; D016227:Benzoquinones / Q000737:chemistry*; D002417:Cattle; D018360:Crystallography, X-Ray; D003573:Cytochrome b Group / Q000737:chemistry; D014450:Electron Transport Complex III / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D004791:Enzyme Inhibitors / Q000737:chemistry*; D006912:Hydroxyquinolines / Q000737:chemistry; D008929:Mitochondria, Heart / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D011485:Protein Binding; D011487:Protein Conformation; D021122:Protein Subunits / Q000737:chemistry; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014451:Ubiquinone / Q000737:chemistry
chemical_list: D016227:Benzoquinones; D003573:Cytochrome b Group; D004791:Enzyme Inhibitors; D006912:Hydroxyquinolines; D021122:Protein Subunits; D014451:Ubiquinone; C010494:nonyl-4-hydroxyquinoline-N-oxide; C004532:quinone; D000968:Antimycin A; D014450:Electron Transport Complex III