Plasticity of the Quinone-binding Site of the Complex II Homolog Quinol:Fumarate Reductase

Singh, Prashant K.; Sarwar, Maruf; Maklashina, Elena; Kotlyar, Violetta; Rajagukguk, Sany; Tomasiak, Thomas; Cecchini, Gary; Iverson, T.M.

doi:10.1074/jbc.m113.487082

Cited by 9 publications

(7 citation statements)

References 46 publications

(74 reference statements)

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“…Kinetic measurements and docking studies of site specific mutations at the quinone binding site revealed that the ubiquinone and the menaquinone reduction does not take the same pathway for the proton transfer confirming that the site accommodates to the type of quinone used [55]. Importantly, not an individual residue functions as a partner for proton uptake; but several residues seem to be able to take this role.…”

Section: Accommodation Of Different Quinone Types In E Coli Complexesmentioning

confidence: 96%

“…Importantly, not an individual residue functions as a partner for proton uptake; but several residues seem to be able to take this role. The flexibility of the quinone binding site was then suggested to be an evolutionarily conserved mechanism not only for maximizing, but also for regulating respiratory function [55].…”

Section: Accommodation Of Different Quinone Types In E Coli Complexesmentioning

confidence: 99%

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Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Hellwig

2015

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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In bioenergetic systems quinones play a central part in the coupling of electron and proton transfer. The specific function of each quinone binding site is based on the protein-quinone interaction that can be described by means of reaction induced FTIR difference spectroscopy, induced for example by light or electrochemically. The identification of sites in enzymes from the respiratory chain is presented together with the analysis of the accommodation of different types of quinones to the same enzyme and the possibility to monitor the interaction with inhibitors. Reaction induced FTIR difference spectroscopy is shown to give an essential information on the general geometry of quinone binding sites, the conformation of the ring and of the substituents as well as essential structural information on the identity of the amino-acid residues lining this site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

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Section: Accommodation Of Different Quinone Types In E Coli Complexesmentioning

confidence: 96%

Section: Accommodation Of Different Quinone Types In E Coli Complexesmentioning

confidence: 99%

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Hellwig

2015

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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“…It has been suggested that the quinone-binding pockets in these enzymes have a plastic structure, not a rigid structure as described by the so-called "lock and key" analogy. 31) Therefore, the NH-form of pyflubumide and the OHform of cyenopyrafen may share a common binding pocket but bind in different manners, as revealed for inhibitors that bind to the Q o site of complex III. 32) …”

Section: Comparison Of the Nh-form Of Pyflubumide With Anmentioning

confidence: 99%

Mode of action of novel acaricide pyflubumide: Effects on the mitochondrial respiratory chain

Nakano

Yasokawa

Suwa

et al. 2015

Journal of Pesticide Science

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This study aimed to determine the mode of action of pyflubumide, a novel acaricide under development by Nihon Nohyaku Co., Ltd. Because of its structural similarity to succinate-dehydrogenase inhibitor (SDHI) fungicides, its ability to inhibit mitochondrial complex II was investigated. Pyflubumide exhibited low inhibitory activity on spider mite mitochondria; conversely, its deacylated metabolite (NH-form) showed high mitochondrial inhibitory activity. Pyflubumide was quickly metabolized to its NH-form in the homogenate of spider mites. These results suggest that pyflubumide is a prodrug and that the NH-form is active. Indeed, the NH-form of pyflubumide and the OH-form of cyenopyrafen, a complex II inhibitory acaricide, act on the same enzyme; a double-inhibitor titration assay showed that the binding sites on mitochondrial complex II and/or the manners of binding of these compounds exhibit clear differences. This finding suggests that these two acaricides should be classified into different groups in terms of their mode of action.

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“…Hence, only af ew high-resolution crystal structures of these complexes with bound quinones are available and the characterization of structural modifications occurring in the Qs ite during enzymet urnover remains challenging. [9] In this context, spectroscopict echniques such as electron paramagnetic resonance(EPR)and in particular hyperfine spectroscopies for example, electron nuclear double resonance (ENDOR), electron spin echo envelopem odulation (ESEEM) spectroscopy,a nd its two-dimensional variant hyperfine sublevel correlation (HYSCORE) spectroscopy are powerful in providing high-resolution structural data on SQ intermediates in bioenergetic complexes. [5,10,11] They allow the detection of magnetic nuclei (e.g.,n aturally abundant 1 Ha nd 14 N) located in the immediate vicinity of the radicals uch as those belongingt o the quinone itself, to the solvent, or to nearby amino acids.…”

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confidence: 99%

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective ²H and ¹⁵N Labeling, HYSCORE Spectroscopy, and DFT Modeling

et al. 2017

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In vivo specific isotope labeling at the residue or substituent level is used to probe menasemiquinone (MSK) binding to the quinol oxidation site of respiratory nitrate reductase A (NarGHI) from E. coli. 15N selective labeling of His15Nδ or Lys15Nζ in combination with hyperfine sublevel correlation (HYSCORE) spectroscopy unambiguously identified His15Nδ as the direct hydrogen‐bond donor to the radical. In contrast, an essentially anisotropic coupling to Lys15Nζ consistent with a through‐space magnetic interaction was resolved. This suggests that MSK does not form a hydrogen bond with the side chain of the nearby Lys86 residue. In addition, selective 2H labeling of the menaquinone methyl ring substituent allows unambiguous characterization of the 2H—and hence of the 1H—methyl isotropic hyperfine coupling by 2H HYSCORE. DFT calculations show that a simple molecular model consisting of an imidazole Nδ atom in a hydrogen‐bond interaction with a MSK radical anion satisfactorily accounts for the available spectroscopic data. These results support our previously proposed one‐sided binding model for MSK to NarGHI through a single short hydrogen bond to the Nδ of His66, one of the distal heme axial ligands. This work establishes the basis for future investigations aimed at determining the functional relevance of this peculiar binding mode.

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Plasticity of the Quinone-binding Site of the Complex II Homolog Quinol:Fumarate Reductase

Cited by 9 publications

References 46 publications

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Mode of action of novel acaricide pyflubumide: Effects on the mitochondrial respiratory chain

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective ²H and ¹⁵N Labeling, HYSCORE Spectroscopy, and DFT Modeling

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Plasticity of the Quinone-binding Site of the Complex II Homolog Quinol:Fumarate Reductase

Cited by 9 publications

References 46 publications

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Mode of action of novel acaricide pyflubumide: Effects on the mitochondrial respiratory chain

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective 2H and 15N Labeling, HYSCORE Spectroscopy, and DFT Modeling

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Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective ²H and ¹⁵N Labeling, HYSCORE Spectroscopy, and DFT Modeling