Steady-State Kinetics of NADH:coenzyme Q Oxidoreductase Isolated from Bovine Heart Mitochondria

Steady-state kinetics of the bovine heart NADH:coenzyme Q oxidoreductase reaction were analyzed in the presence of various concentrations of NADH and coenzyme Q with one isoprenoid unit (Q₁). Product inhibitions by NAD⁺ and reduced coenzyme Q₁ were also determined. These results show an ordered sequential mechanism in which the order of substrate binding and product release is Q₁–NADH–NAD⁺–Q₁H₂. It has been widely accepted that the NADH binding site is likely to be on the top of a large extramembrane portion protruding to the matrix space while the Q₁ binding site is near the transmembrane moiety. The rigorous controls for substrate binding and product release are indicative of a strong, long range interaction between NADH and Q₁ binding sites.     

The second coenzyme Q1 binding site of bovine heart NADH: coenzyme Q oxidoreductase

The rotenone sensitivity of bovine heart NADH: coenzyme Q oxidoreductase (Complex I) depends significantly on coenzyme Q₁ concentration. The rotenone-insensitive Complex I reaction in Q₁ concentration range above 300 M indicates an ordered sequential mechanism with Q₁ and reduced Q₁ (Q₁H₂) as the initial substrate to bind to the enzyme and the last product to be released from the enzyme product complex, respectively. This is the case in the rotenone-sensitive reaction although both K _m and V _max values of the rotenone-insensitive reaction for Q₁ are significantly higher than those of the rotenone-sensitive reaction (Nakashima et al., 2002, J. Bioenerg. Biomemb. 34, 11–19). This rigorous control mechanism between the nucleotide and ubiquinone binding sites strongly suggests that the rotenone-insensitive reaction is also physiologically relevant.     

Studies on reduced and oxidized coenzyme Q (ubiquinones). II. The determination of oxidation-reduction levels of coenzyme Q in mitochondria,microsomes and plasma by high-performance liquid chromatography

Reduced and oxidized coenzyme Q₁₀ (Q₁₀H₂ and Q₁₀) in guinea-pig liver mitochondria were rapidly extracted and determined by high-performance liquid chromatography (HPLC). The percentages of Q₁₀H₂ as compared to the total (sum of Q₁₀ and Q₁₀H₂) were increased by the addition of respiratory substrates such as succinate, malate and β-hydroxybutyrate (State 4). The levels of Q₁₀H₂ in State 4 were increased more extensively with electron-transport inhibitors such as KCN, NaN₃ and antimycin A. These results indicate that the method for determining Q₁₀H₂ and Q₁₀ by HPLC is quite useful for investigation of the physiological function of coenzyme Q in mitochondria and other organelles. The reduced and oxidized coenzyme Q levels of rat liver mitochondria, which contain both coenzyme Q₉ and coenzyme Q₁₀, were measured simultaneously. The results suggest that coenzymes Q₉ and Q₁₀ play a similar role as an electron carriers. The liver microsomes of guinea-pig contained approx. 133 nmol total coenzyme Q₁₀ per g protein. The Q₁₀H₂ levels of microsomes were increased from 46.5 to 67.5 and 64.8% with NADH and NADPH, respectively. The plasma levels of total coenzyme Q were 0.92 μg/ml for man, 0.35 μg/ml for guinea-pig and 0.27 μg/ml for rat. The reduced coenzyme Q were also present in those plasma samples. The levels of reduced coenzyme Q were 51.1, 48.9 and 65.3%, respectively.     

The thermotropic properties of coenzyme Q10 and its lower homologues

The thermotropic properties of coenzymes Q₁₀, Q₉, Q₈, and Q₇ have been examined by differential scanning calorimetry and wide-angle X-ray diffraction. Typical scanning calorimetry cooling curves of coenzyme Q from the liquid state exhibit a single exothermic phase transition into a crystalline state at a temperature that decreases as the length of the polyisoprenoid side-chain substituent decreases. Upon subsequent heating, the molecules undergo a series of thermal events which precede the main crystalline-to-liquid endothermic phase transition. The temperature of these transitions increases with increasing chain length. The crystallization phase transition temperature depends markedly on the rate at which the sample is cooled and increases with decreasing scan rate; the temperature of the melting endotherm is not markedly affected by the scan rate. Detailed calorimetric studies of coenzyme Q₁₀ indicate that two crystalline states are formed, one at relatively high cooling rates to low temperatures and the other when preparations are cooled slowly from the liquid state to relatively high temperatures. Heating the crystalline phase formed by rapid cooling causes its transformation into the phase observed by cooling slowly. X-ray diffraction analysis confirmed the existence of these two crystal phases in coenzymes Q₉ and Q₁₀ and the transformation from the rapidly crystallized form to the more ordered form associated with slower cooling rates. At body temperature (310 K) under equilibrium conditions coenzyme Q₁₀ exists in an ordered crystalline phase; the implications of the thermotropic behavior of coenzyme Q₁₀ on mitochondrial functionin vitro andin vivo are discussed.     

Effect of pH on the Steady State Kinetics of Bovine Heart NADH: Coenzyme Q Oxidoreductase

Complete initial steady state kinetics of NADH-decylubiquinone (DQ) oxidoreductase reaction between pH 6.5 and 9.0 show an ordered sequential mechanism in which the order of substrate bindings and product releases is NADH-DQ–DQH₂-NAD⁺. NADH binding to the free enzyme is accelerated by protonation of an amino acid (possibly a histidine) residue. The NADH release is negligibly slow under the turnover conditions. The rate of DQ binding to the NADH-bound enzyme and the maximal rate at the saturating concentrations of the two substrates, which is determined by the rates of DQH₂ formation in the active site and releases of DQH₂ and NAD⁺ from the enzyme, are insensitive to pH, in contrast to clear pH dependencies of the maximal rates of cytochrome c oxidase and cytochrome bc ₁ complex. Physiological significances of these results are discussed.     

Interactions Between Ascorbyl Free Radical and Coenzyme Q at the Plasma Membrane

A role for coenzyme Q in the stabilization of extracellular ascorbate by intact cells has beenrecently recognized. The aim of this work was to study the interactions between reducedubiquinone in the plasma membrane and the ascorbyl free radical, as an approach to understandubiquinone-mediated ascorbate stabilization at the cell surface. K-562 cells stabilized ascorbateand decreased the steady-state levels of the semiascorbyl radical. The ability of cells to reduceascorbyl free radical was inhibited by the quinone analogs capsaicin and chloroquine andstimulated by supplementing cells with coenzyme Q₁₀. Purified plasma membranes also reducedascorbyl free radical in the presence of NADH. Free-radical reduction was notobserved inquinone-depleted plasma membranes, but restored after its reconstitution with coenzyme Q₁₀.Addition of reduced coenzyme Q₁₀ to depleted membranes allowed them toreduce the signalof the ascorbyl free radical without NADH incubation and the addition of an extra amount ofpurified plasma membrane quinone reductase further stimulated this activity. Reduction wasabolished by treatment with the reductase inhibitor p-hydroximercuribenzoate and by blockingsurface glycoconjugates with the lectin wheat germ agglutinin, which supports the participationof transmembrane electron flow. The activity showed saturation kinetics by NADH andcoenzyme Q, but not by the ascorbyl free radical in the range of concentrations used. Our resultssupport that reduction of ascorbyl free radicals at the cell surface involves coenzyme Qreduction by NADH and the membrane-mediated reduction of ascorbyl free radical.     

The site of inhibition of mitochondrial electron transfer by coenzyme Q analogues.

The effects of 33 quinone derivatives on mitochondrial electron transfer in yeast were examined. Twenty-two of the compounds were also tested for their effects on the growth of yeast cells. Four strong inhibitors of electron transfer were identified: 5-n-undecyl-6-hydroxy-4, 7-dioxobenzothiazole, 7-ω-cyclohexyloctyl-6-hydroxy-5,8-quinolinequinone, 7-n-hexadecyl-mercapto-6-hydroxy-5, 8-quinolinequinone, and 3-n-dodecylmercapto-2-hydroxy-1, 4-naphthoquinone. They inhibit the growth of yeast with ethanol as an energy source, but not when glucose is the energy source. The NADH oxidase activity of isolated mitochondria is 50% inhibited by these quinone derivatives at about 10^?8m, or 0.5 μmol/g mitochondrial protein; 1000-fold higher concentrations do not affect electron transfer from NADH or succinate to coenzyme Q₂. The effects of the inhibitors on cytochrome spectra indicate that they block electron transfer between cytochromes b and c₁. A possible antagonism between these compounds and coenzyme Q at a site between cytochromes b and C₁ is discussed in terms of Mitchell's “protonmotive Q cycle” hypothesis (Mitchell, P. (1976) J. Theor. Biol. 62, 327–367). 6-β-naphthylmercapto-5-chloro-2,3-dimethoxy-1,4-benzoquinone inhibits electron transfer between succinate and coenzyme Q₂ or phenazine methosulfate, suggesting a site in the succinate-coenzyme Q reductase complex with a different quinone specificity from that of the site in the cytochrome bc₁ complex. Seven of the quinone derivatives inhibit growth on both glucose and ethanol media, indicating that their effect is not the result of inhibition of respiration.     

Coordinated, coenzyme Q reversible, 2,5-dibromothymoquionine inhibition of electron transport and ATPase in Escherichia coli.

2,6-dibromothymoquinone (DBMIB) and other coenzyme Q analogs partially inhibit electron transport and the membrane-bound Mg⁺⁺ stimulated ATPase of $\text{E. coli}$ membranes. The inhibitions by DBMIB are fully reversed by coenzyme Q₆, and other analogs show partial reversal by coenzyme Q₆. Electron transport reactions inhibited are NADH and lactate oxidase, NADH menadione reductase, lactate phenazinemethosulfate reductase and duroquinol oxidase. The concentrations of DBMIB required are similar for electron transport and ATPase inhibition and inhibitions are all increased by uncouplers. Electron transport and ATPase are not inhibited in a DBMIB insensitive mutant. Soluble ATPase extracted from the membranes does not show DBMIB inhibition under either high or low Mg⁺⁺ conditions. Lipophilic chelators show additional inhibition over DBMIB. It appears that coenzyme Q functions at three sites in $\text{E. coli}$ electron transport where ATPase activity is controlled. Coenzyme Q deficient mutants also show decreased electron transport and ATPase activity which is restored by coenzyme Q.     

Essentiality of coenzyme Q for the oxidation of -glycerophosphate by pig brain mitochondria

Serial extraction of lyophilized pig brain mitochondria with cold pentane resulted in complete loss of α-glycerophosphate oxidase activity. On titration with coenzyme Q₁₀ the activity was fully recovered. On comparing the decline of α-glycerophosphate, NADH, and succinoxidase activities during serial extraction with pentane, α-glycerophosphate oxidation was always the first to be lost. Extraction of coenzyme Q₁₀ from lyophilized brain mitochondria with pentane does not affect the activities of α-glycerophosphate or NADH dehydrogenase, but succinate dehydrogenase is partially inactivated. Reversible inactivation of the α-glycerophosphate oxidase system on depletion of the coenzyme Q content is taken as evidence that coenzyme Q is an obligatory component of this system. In accord with the conclusion that coenzyme Q is probably the physiological oxidant of α-glycerophosphate dehydrogenase, in antimycin-treated brain mitochondria α-glycerophosphate causes full activation of endogenous succinate dehydrogenase, in analogy to the previously observed activation by NAD-linked substrates in liver and heart mitochondria and by NADH in submitochondrial particles.     

On the Partly Reduced Coenzyme Q Isolated from “Rhodotorula lactose” IFO 1058 and Its Relation to the Taxonomic Position

From the intact cells of “Rhodotorula lactosa” R1 (IFO 1058), a new coenzyme Q, which has a different mobility on paper chromatograms from other five naturally occurring homologs of the coenzyme Q series, was isolated and purified as a crystalline state. The chemical analyses such as UV and IR absorption spectrophotometries, and NMR and mass spectrometries revealed that the material, mp 28.7~28.9°C, was identified as a Co Q₁₀ derivative with the reduced C₅ unit in the isoprenoid side chain terminal remote from the quinone nucleus, Co Q₁₀ (H–10). The strain R 1 with such a unique coenzyme Q system is, concerning its taxonomic position, discussed in connection with other criteria.     

Coenzyme Q distribution in HL-60 human cells depends on the endomembrane system

Coenzyme Q (Q) is an essential factor in the mitochondrial electron chain but also exerts important antioxidant functions in the rest of cell membranes of aerobic organisms. However, the mechanisms of distribution of Q among cell membranes are largely unclear. The aim of the present work is to study the mechanisms of distribution of endogenous Q₁₀ and exogenous Q₉ among cell membranes in human HL-60 cells. Endogenous Q₁₀ synthesized using the radiolabelled precursor [¹⁴C]-pHB was first detected in mitochondria, and it was later incorporated into mitochondria-associated membranes and endoplasmic reticulum (ER). Plasma membrane was the last location to incorporate [¹⁴C]-Q₁₀. Brefeldin A prevented Q₁₀ incorporation in plasma membrane. Exogenous Q₉ was preferably accumulated into the endo-lysosomal fraction but a significant amount was distributed among other cell membranes also depending on the brefeldin-A-sensitive endomembrane system. Our results indicate that mitochondria are the first location for new synthesized Q. Exogenous Q is mainly incorporated into an endo-lysosomal fraction, which is then rapidly incorporated to cell membranes mainly to MAM and mitochondria. We also demonstrate that both endogenous and dietary Q is distributed among endomembranes and plasma membrane by the brefeldin A-sensitive endo-exocytic pathway.     

Comparison of growth stimulation of HeLa cells,HL-60 cells,and mouse fibroblasts by coenzyme Q10

Summary The addition of coenzyme Q₁₀ to culture media stimulates the serum-free growth of HeLa, HL-60 cells, and mouse fibroblasts (Balb/3T3). With HeLa cells, the stimulation by coenzyme Q₁₀ is additive to the stimulation by ferricyanide, an impermeable electron acceptor for the transplasma membrane electron transport. This combined response to coenzyme Q₁₀ and ferricyanide is enhanced with insulin. -Tocopherylquinone can also stimulate the growth of HeLa cells, but vitamin K₁ is inactive. Specificity of quinone effects is indicated. Serum-free growth of Balb/3T3 and SV 40 transformed BaIb/3T3 (SV/T2) cells is also stimulated by coenzyme Qio with stimulation similar to HeLa cells. However, Balb/3T3 cells are not stimulated by ferricyanide, which does not increase the response to coenzyme Q₁₀. The transformed cells (SV/T2) respond better to ferricyanide alone, but the effects of coenzyme Qio and ferricyanide are not additive. Serum-free growth of HL-60 cells is stimulated dramatically by coenzyme Q₁₀. The extent of growth stimulation on HL-60 cells is almost six-fold that of HeLa or Balb/3T3 cells. The stimulation of NADH-ferricyanide reductase (a transmembrane redox enzyme) by coenzyme Q₁₀ with HL-60 cells is similar to their growth pattern in response to coenzyme Q₁₀. Unlike HL-60, HeLa and Balb/3T3 cells show little stimulation of ferricyanide reduction by coenzyme Q₁₀. The stimulatory effect on both ferricyanide reduction and cell growth by the short side-chain coenzyme Q₂ is much less than that of the long side-chain coenzyme Q₁₀. Ferricyanide reduction by HeLa cells is inhibited by coenzyme Q analogs such as 2,3-dimethoxy-5-chloro-6-naphthyl-mercapto-coenzyme Q and 2-methoxy-3-ethoxyl-5-methyl-6-hexadecyl-mercapto-coenzyme Q. However, these inhibitions are reversed by coenzyme Q₁₀. The growth inhibition of HL-60 cells by other coenzyme Q analogs, such as capsiacin can also be reversed by coenzyme Q₁₀. These data indicate that plasma membrane-based NADH oxidation or modification of the membrane quinone redox balance may be a basis for the growth stimulation.     

Ockham's razor gone blunt: coenzyme Q adaptation and redox balance in tropical reef fishes

The ubiquitous coenzyme Q (CoQ) is a powerful antioxidant defence against cellular oxidative damage. In fishes, differences in the isoprenoid length of CoQ and its associated antioxidant efficacy have been proposed as an adaptation to different thermal environments. Here, we examine this broad contention by a comparison of the CoQ composition and its redox status in a range of coral reef fishes. Contrary to expectations, most species possessed CoQ₈ and their hepatic redox balance was mostly found in the reduced form. These elevated concentrations of the ubiquinol antioxidant are indicative of a high level of protection required against oxidative stress. We propose that, in contrast to the current paradigm, CoQ variation in coral reef fishes is not a generalized adaptation to thermal conditions, but reflects species-specific ecological habits and physiological constraints associated with oxygen demand.     

Conformation of coenzyme fragments when bound to lactate dehydrogenase

The conformations of adenosine, 5′-AMP and 5′-ADP when bound to dogfish M₄ lactate dehydrogenase at pH 7.8 or greater have been determined at 2.8 Å resolution to investigate the events on coenzyme binding. The coenzyme fragments AMP and ADP induce a conformational change in lactate dehydrogenase at pH values less than 6.0 in the same way as do NAD⁺, NADH or ADPR at any pH value. The structure of NAD⁺ when bound to lactate dehydrogenase had previously been determined at 5.0 Å resolution. The structures of the bound adenosine, AMP, ADP and NAD⁺ are compared with the preliminary structure of NAD in a 3.0 Å resolution map of the ternary complex LDH-NAD—pyruvate. Small but significant changes in the binding of the phosphates could be important in the folding of the protein loop over the substrate binding pocket.     

Modes of coenzyme Q function in electron transfer

Summary In the mitochondrial respiratory chain, coenzyme Q acts in different ways. A diffusable coenzyme Q pool as a common substrate-like intermediate links the low-potential complexes with complex III. Its diffusion in the lipids is not rate-limiting for electron transfer, but its content is not saturating for maximal rate of NADH oxidation. Protein-bound coenzyme Q is involved in energy conservation, and may be part of enzyme supercomplexes, as in succinate cytochromec reductase. The reason for lack of kinetic saturation of the respiratory chain by quinone concentration is in the low extent of solubility of monomeric coenzyme Q in the membrane lipids. Assays of respiratory enzymes are performed using water soluble coenzyme Q homologs and analogs; several problems exist in using oxidized quinones as acceptors of coenzyme Q reductases. In particular, for complex I no acceptor appears to favorably substitute the endogenous quinone. In addition, quinone reduction sites in complex III compete with the sites in the dehydrogenases, particularly when using duroquinone. The different extent by which these sites operate when different donor substrates (NADH, succinate, glycerol-3-phosphate) are used is best explained by different exposure of the quinone acceptor sites in the dehydrogenases.     

The inhibition of NADH oxidase by the lower homologs of coenzyme Q.

The Coenzyme Q homologs having short isoprenoid chains are much less efficient than the higher homologs in restoring NADH oxidation in pentane-extracted lyophilized beef heart mitochondria; they have however high restoring activity for succinate oxidation. The same pattern is observed in pentane extracted submitochondrial particles ETP only if the quinones are added to detergent-treated membranes, showing that in ETP there is a decreased accessibility of the long chain quinones in comparison with the lower homologs. In intact mitochondria and ETP, CoQ₃ inhibits NADH oxidation while leaving succinate oxidation unaffected; the inhibition of NADH oxidation by CoQ₃ is not reversed by serum albumin but is reversed by CoQ₇, particularly when the membrane has been previously “opened” with deoxycholate. CoQ₃ may accept electrons from NADH in cyanide-inhibited ETP, allowing coupling at the first phosphorylation site as shown by the quenching of the fluorescence of atebrine. The mechanism of CoQ₃ inhibition is probably related to its insufficient rate of reoxidation by the following segment of the respiratory chain when it has been reduced by NADH dehydrogenase.     

Conformational effects of coenzyme binding to porcine lactic dehydrogenase

Changes induced on addition of the coenzyme, NADH or NAD⁺, to porcine lactic dehydrogenase isoenzymes H₄ and M₄ have been studied by hydrodynamic and spectroscopic methods. As shown by ultracentrifugal analysis, the native subunit structure remains unchanged on holoenzyme formation; a 5% increase of the sedimentation coefficient, parallelled by a slight decrease of the partial specific volume (<1%) indicate a significant change in the native tertiary and/or quaternary structure of the enzymes, corroborating earlier calorimetric data (Hinz and Jaenicke, 1975). The binding constant for the enzyme from skeletal muslce (M₄) and NADH are found to be in agreement with K _D-values obtained from equilibrium dialysis, as well as spectroscopic and thermal titration experiments (8 M). Far UV circular dichroism measurements do not show significant changes on ligand binding, indicating unchanged helicity or compensatory conformational effects. In the near UV, ligand binding is reflected by an extrinsic Cotton effect around 340 nm; in the range of aromatic absorption no changes are detectable.The experimental results suggest that there are gross structural changes on coenzyme binding to lactic dehydrogenase which do not affect the intrinsic spectral properties normally applied to analyze transconformation reactions in protein molecules.     

On coenzyme Q orientation in membranes: A linear dichroism study of ubiquinones in a model bilayer

Summary A general approach is developed to interpret linear dichroism (LD) spectra of ubiquinones (Q _n) in host bilayers. Information is reported in terms of guest-host mutual orientation and localization. The overall orientational anisotropy of guest ubiquinone molecules is described by a basic set of limiting orientation/localization modes. Assignments of the UV transitions of the ubiquinone chromophore were obtained by the liquid crystal-linear dichroism technique and molecular orbital (CNDO/S) calculations. The LD spectra of Q _n in the bilayers provided by the lyotropic nematic mesophase exhibited by water solutions of potassium laurate and decanol were interpreted on the basis of the above assignments. The resulting experimental evidence showed a multisite distribution in the host bilayer for the aromatic heads of all the investigated Q _n derivatives except Q₀. The orientational distribution suggested by the LD spectra fits the solubilization model recently proposed by G. Lenaz [J. Membrane Biol. (1988) 104:193–209] for ubiquinone in lipid membranes. Within this model Q _n molecules are located in the midplane and their headgroups oscillate transversally across the membrane. Q ₀ instead has a single site location, close to the polar bilayer interface. Experimental evidence that the headgroup carbonyls tend to grasp the polar interface of the host bilayer was also obtained. Orientation and location distributions of Q _n guest molecules are therefore likely to result from the tendency of their aromatic heads to grasp the polar heads of the host bilayer and from the concurrent tendency of their chains to settle into the hydrocarbon host interior.abbreviations AA average absorption - OD, OD optical densities for plane polarized radiations parallel () and perpendicular () to the sample optical axis - OD OD — OD - EPR electron paramagnetic resonance - LC-LD liquid crystal-linear dichroism - LD linear dichroism - LD _r reduced linear dichroism. - MO molecular orbital - N nematic - NMR nuclear magnetic resonance - S _jj order parameters of the directions j of the transition moments of the guest chromophore - S _ii order parameters of the orientational axes i of the guest molecule with respect to the magnetic field - S _ii order parameters of the axes i of the guest molecules with respect to the bilayer axis a - S _a order parameters of the host bilayer axis a with respect to the orienting magnetic field - _j,i deflection angles between the directions j and the axes i - O _i optical factors of the i axis see Eq. (A4)] - Q_n ubiquinone whose isoprenoid chain contains n isoprenoid units Dr. A. Rossi is gratefully acknowledged for the t.e.m. reduction of the spectra. Ubiquinone homologs were kind gifts from Eisai Co., Tokyo, Japan. This work was supported by M.U.R.S.T., and C.N.R. Target Project on Biotechnology and Bioinstrumentation, Rome, Italy.     

1,2H hyperfine spectroscopy and DFT modeling unveil the demethylmenasemiquinone binding mode to E. coli nitrate reductase A (NarGHI)

The quinol oxidation site Q_D in E. coli respiratory nitrate reductase A (EcNarGHI) reacts with the three isoprenoid quinones naturally synthesized by the bacterium, i.e. ubiquinones (UQ), menaquinones (MK) and demethylmenaquinones (DMK). The binding mode of the demethylmenasemiquinone (DMSK) intermediate to the EcNarGHI Q_D quinol oxidation site is analyzed in detail using ^1,2H hyperfine (hf) spectroscopy in combination with H₂O/D₂O exchange experiments and DFT modeling, and compared to the menasemiquinone one bound to the Q_D site (MSK_D) previously studied by us. DMSK_D and MSK_D are shown to bind in a similar and strongly asymmetric manner through a short (~1.7 Å) H-bond. The origin of the specific hf pattern resolved on the DMSK_D field-swept EPR spectrum is unambiguously ascribed to slightly inequivalent contributions from two β-methylene protons of the isoprenoid side chain. DFT calculations show that their large isotropic hf coupling constants (A_iso ~12 and 15 MHz) are consistent with both (i) a specific highly asymmetric binding mode of DMSK_D and (ii) a near in-plane orientation of its isoprenyl chain at Cβ relative to the aromatic ring, which differs by ~90° to that predicted for free or NarGHI-bound MSK. Our results provide new insights into how the conformation and the redox properties of different natural quinones are selectively fine-tuned by the protein environment at a single Q site. Such a fine-tuning most likely contributes to render NarGHI as an efficient and flexible respiratory enzyme to be used upon rapid variations of the Q-pool content.     

Structural determinants in bacterial 2‐keto‐3‐deoxy‐D‐gluconate dehydrogenase KduD for dual‐coenzyme specificity

Short‐chain dehydrogenase/reductase (SDR) is distributed in many organisms, from bacteria to humans, and has significant roles in metabolism of carbohydrates, lipids, amino acids, and other biomolecules. An important intermediate in acidic polysaccharide metabolism is 2‐keto‐3‐deoxy‐d ‐gluconate (KDG). Recently, two short and long loops in Sphingomonas KDG‐producing SDR enzymes (NADPH‐dependent A1‐R and NADH‐dependent A1‐R′) involved in alginate metabolism were shown to be crucial for NADPH or NADH coenzyme specificity. Two SDR family enzymes—KduD from Pectobacterium carotovorum (PcaKduD) and DhuD from Streptococcus pyogenes (SpyDhuD)—prefer NADH as coenzyme, although only PcaKduD can utilize both NADPH and NADH. Both enzymes reduce 2,5‐diketo‐3‐deoxy‐d ‐gluconate to produce KDG. Tertiary and quaternary structures of SpyDhuD and PcaKduD and its complex with NADH were determined at high resolution (approximately 1.6 Å) by X‐ray crystallography. Both PcaKduD and SpyDhuD consist of a three‐layered structure, α/β/α, with a coenzyme‐binding site in the Rossmann fold; similar to enzymes A1‐R and A1‐R′, both arrange the two short and long loops close to the coenzyme‐binding site. The primary structures of the two loops in PcaKduD and SpyDhuD were similar to those in A1‐R′ but not A1‐R. Charge neutrality and moderate space at the binding site of the nucleoside ribose 2′ coenzyme region were determined to be structurally crucial for dual‐coenzyme specificity in PcaKduD by structural comparison of the NADH‐ and NADPH‐specific SDR enzymes. The corresponding site in SpyDhuD was negatively charged and spatially shallow. This is the first reported study on structural determinants in SDR family KduD related to dual‐coenzyme specificity. Proteins 2016; 84:934–947. © 2016 Wiley Periodicals, Inc.