The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli

Yap, Lai Lai; Lin, Myat T.; Ouyang, Hanlin; Samoilova, Rimma I.; Dikanov, Sergei A.; Gennis, Robert B.

doi:10.1016/j.bbabio.2010.04.011

Cited by 46 publications

(98 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sato-Watanabe et al [31] postulated that the QH site serves as a transient electron reservoir for the two-electron supply from the low affinity site (QL) and gates electron transfer, allowing sequential one-electron transfer from the QL site to heme b. In an alternative explanation the second bound quinone seems to be able to rapidly exchange with the substrate pool [37]. The QL site was proposed to be located close to the QH site [37] by EPR spectroscopies or in the C-terminal hydrophilic domain of subunit II by photoaffinity cross-linking [38,39] and mutagenesis studies [40,41].…”

Section: Identification Of Binding Sitesmentioning

confidence: 99%

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Hellwig

2015

Biochimica et Biophysica Acta (BBA) - Bioenergetics

View full text Add to dashboard Cite

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.

show abstract

Section: Identification Of Binding Sitesmentioning

confidence: 99%

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Hellwig

2015

Biochimica et Biophysica Acta (BBA) - Bioenergetics

View full text Add to dashboard Cite

show abstract

“…Similar to other heme-copper oxidases, cyt bo 3 couples the energy available from the electron transfer reaction to the translocation of protons across the cytoplasmic membrane (15). The enzyme contains two quinone binding sites known as the low affinity site (Q L ) and the high affinity site (Q H ) (16). The Q L site functions as the substrate binding site, whereas a UQ cofactor is tightly bound at the Q H site and is stabilized as an SQ intermediate during the reaction that can be detected by EPR (17,18).…”

mentioning

confidence: 99%

Exploring by Pulsed EPR the Electronic Structure of Ubisemiquinone Bound at the QH Site of Cytochrome bo3 from Escherichia coli with in Vivo 13C-Labeled Methyl and Methoxy Substituents

Lin

Shubin

Samoilova

et al. 2011

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The cytochrome bo 3 ubiquinol oxidase from Escherichia coli resides in the bacterial cytoplasmic membrane and catalyzes the two-electron oxidation of ubiquinol-8 and four-electron reduction of O 2 to water. The one-electron reduced semiquinone forms transiently during the reaction, and the enzyme has been demonstrated to stabilize the semiquinone. The semiquinone is also formed in the D75E mutant, where the mutation has little influence on the catalytic activity, and in the D75H mutant, which is virtually inactive. In this work, wild-type cytochrome bo 3 as well as the D75E and D75H mutant proteins were prepared with ubiquinone-8 13 C-labeled selectively at the methyl and two methoxy groups. This was accomplished by expressing the proteins in a methionine auxotroph in the presence of L-methionine with the side chain methyl group 13 C-labeled. The 13 Clabeled quinone isolated from cytochrome bo 3 was also used for the generation of model anion radicals in alcohol. Two-dimensional pulsed EPR and ENDOR were used for the study of the 13 C methyl and methoxy hyperfine couplings in the semiquinone generated in the three proteins indicated above and in the model system. The data were used to characterize the transferred unpaired spin densities on the methyl and methoxy substituents and the conformations of the methoxy groups. In the wild type and D75E mutant, the constraints on the configurations of the methoxy side chains are similar, but the D75H mutant appears to have altered methoxy configurations, which could be related to the perturbed electron distribution in the semiquinone and the loss of enzymatic activity. Ubiquinone (UQ)3 functions as a membrane-soluble twoelectron carrier. It is often found as a cofactor in many respiratory and photosynthetic complexes and plays an important role in biological oxidation-reduction reactions. Many of these reactions consist of one-electron transfer steps and involve the one-electron reduced ubisemiquinone species as the intermediates. Knowledge of how the semiquinone (SQ) radicals are stabilized in these complexes is critical to understand their reaction mechanisms. The quinone binding sites located in the respiratory and photosynthetic enzymes are significantly different (1), and each protein fine tunes the properties of the bound quinone cofactor by providing a unique environment in order to accomplish its own electron transfer process (2). The well characterized quinone binding sites include those from bacterial photosynthetic reaction centers (3), cytochrome bo 3 ubiquinol oxidase (cyt bo 3 ) from Escherichia coli (4), cytochrome bc 1 complexes (5), photosystems I and II, and some others (6 -9).A SQ can bind within a protein site in a manner that favors either the neutral (QH ⅐ ) or anionic (Q . ) form or intermediate states with partial charge remaining on the SQ. The proton locations along the hydrogen bonds to the quinone carbonyls determine the net charge on the SQ. The formation of hydrogen bonds of different strengths to the quinone oxygens usually leads to an asym...

show abstract

“…Therefore, by using the parameters given in Tables 1 and 2 and equations (14), (15) and (18), the / ratio, e ciency of oxidative phosphorylation and energy dissipation have been calculated and are shown versus driving force ratio in Figures 1 and 2. For a detailed review and comparison of experimental data with the thermodynamic model, the respiratory enzymes must be speci ed according to the experimental condition.…”

Section: Resultsmentioning

confidence: 99%

“…Given that the e ciency of oxidative phosphorylation and / ratio calculated from the model agree with the experimental results, it can be said that energy dissipation in the oxidative phosphorylation process obeys from the thermodynamic model. Therefore, energy dissipation rate versus force ratio is calculated by using equation (18) and is shown in Figure 3.…”

Section: Resultsmentioning

confidence: 99%

“…Escherichia coli k-12 experimental data in continuous aerobic glucose-limited condition have been used in this study. There are many evidences that under these conditions, the respiratory chain of Escherichia coli k-12 consists of NADH dehydrogenase I and II, cytochrome bo 3 , cytochrome bd and ATP synthase [14][15][16][17][18]. Escherichia coli can synthesize a variety of carriers with respect to growth phase, electron acceptor, carbon source and type of strain.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Investigation of oxidative phosphorylation in continuous cultures. A non-equilibrium thermodynamic approach to energy transduction for Escherichia coli in aerobic condition

Ghafuri

Nosrati

Hosseinkhani

2015

Journal of Non-Equilibrium Thermodynamics

View full text Add to dashboard Cite

Adenosine triphosphate (ATP) production in living cells is very important. Di erent researches have shown that in terms of mathematical modeling, the domain of these investigations is essentially restricted. Recently the thermodynamic models have been suggested for calculation of the e ciency of oxidative phosphorylation process and rate of energy loss in animal cells using chemiosmotic theory and non-equilibrium thermodynamics equations. In our previous work, we developed a mathematical model for mitochondria of animal cells. In this research, according to similarities between oxidative phosphorylation process in microorganisms and animal cells, Golfar's model was developed to predict the non-equilibrium thermodynamic behavior of the oxidative phosphorylation process for bacteria in aerobic condition. With this model the rate of energy loss, / ratio, and e ciency of oxidative phosphorylation were calculated for Escherichia coli in aerobic condition. The results then were compared with experimental data given by other authors. The thermodynamic model had an acceptable agreement with the experimental data.

show abstract

The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli

Cited by 46 publications

References 48 publications

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

Exploring by Pulsed EPR the Electronic Structure of Ubisemiquinone Bound at the QH Site of Cytochrome bo3 from Escherichia coli with in Vivo 13C-Labeled Methyl and Methoxy Substituents

Investigation of oxidative phosphorylation in continuous cultures. A non-equilibrium thermodynamic approach to energy transduction for Escherichia coli in aerobic condition

Contact Info

Product

Resources

About