Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III

Lothar Esser,Fei Zhou,Yihui Zhou,Yumei Xiao,Wai-Kwan Tang,Chang-An Yu,Zhaohai Qin,Di Xia

doi:10.1074/jbc.m116.744391

Abstract

Complex III or the cytochrome (cyt) bc1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc1 is to couple the reaction of electron transfer from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the electron transfer reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation site (QP) of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking. Here we show that the binding of oxazolidinedione-type inhibitors famoxadone, jg144, and fenamidone induces docking of the ISP to the QP site in the absence of the H-bond formation both in mitochondrial and bacterial cyt bc1 complexes, demonstrating that ISP docking is independent of the proposed direct ISP-inhibitor interaction. The binding of oxazolidinedione-type inhibitors to cyt bc1 of different species reveals a toxophore that appears to interact optimally with residues in the QP site. The effect of modifications or additions to the toxophore on the binding to cyt bc1 from different species could not be predicted from structure-based sequence alignments, as demonstrated by the altered binding mode of famoxadone to bacterial cyt bc1.

Highlights

Complex III or the cytochrome bc1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria
It is known that the electron transfer (ET) between the iron-sulfur protein (ISP) and cyt c1 requires movement of the ISP-ED, which could be controlled, as we Differential Inhibition of Mitochondrial and Bacterial cyt bc1 Complexes by Famoxadone—Previously, we reported that binding of famoxadone to bovine mitochondrial cyt bc1 (Btbc1) induces docking of the ISP to the QP site [21]
Doubts that the capture of the ISP-ED induced by famoxadone binding is part of a conserved mechanism were initially cast by the observation that the experimentally determined IC50 values of 1.4 and 418 nM of isolated cyt bc1 from photosynthetic bacterium Rhodobacter sphaeroides (Rsbc1) and mitochondrial cyt bc1 (Btbc1), respectively, differ by a factor of nearly 300 (Fig. 4A)

Summary

Edited by Norma Allewell

Complex III or the cytochrome (cyt) bc complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. Structural studies of bovine mitochondrial cyt bc (Btbc1) in complex with various respiratory inhibitors revealed the inhibitor-type dependent conformation switch of ISP-ED This observation suggested a mechanism for the QH2 oxidation at the QP site and offered a dinedione; NCS, non-crystallographic symmetry; QP, ubiquinol oxidation; QN, ubiquinone reduction; RMS, root mean square; Rsbc, bc1 from photosynthetic bacterium R. sphaeroides; TM, transmembrane; PDB, Protein Data Bank; DDM, dodecyl-D-maltopyranoside; ␤-OG, ␤ octyl glucoside. We used three oxazolidinedione-type inhibitors to form complexes with either mitochondrial or bacterial cyt bc or both and showed that all three inhibitors can induce docking of the ISP-ED at the QP site without forming a direct H-bond with the ISP, which is consistent with the notion that the ISP conformation switch does not require a direct H-bond. It is known that the ET between the ISP and cyt c1 requires movement of the ISP-ED, which could be controlled, as we

Results

Discussion

Space group

Inhibitor class

Structures cyt b

Experimental Procedures