Báo cáo khoa học: Defining the QP-site of Escherichia coli fumarate reductase by site-directed mutagenesis, fluorescence quench titrations and EPR spectroscopy doc

Defining the Q P -site of Escherichia coli fumarate reductase by site-directed mutagenesis, fluorescence quench titrations and EPR spectroscopy Richard A. Rothery 1 , Andrea M. Seime 1 , A M. Caroline Spiers 1 , Elena Maklashina 2,3 , Imke Schro ¨ der 4 , Robert P. Gunsalus 4 , Gary Cecchini 2,3 and Joel H. Weiner 1 1 CIHR Membrane Protein Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada 2 Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, CA, USA 3 Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA 4 Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA Escherichia coli, when grown anaerobically with fuma- rate as the respiratory oxidant, develops a respiratory chain terminated by a membrane-bound menaqui- nol:fumarate oxidoreductase (FrdABCD 1 ) [1,2]. The enzyme comprises a catalytic dimer of the FrdA (65.8 kDa) and FrdB (27 kDa) subunits that is anchored to the inner surface of the cytoplasmic mem- brane by two small hydrophobic membrane-anchor Keywords fumate reductase; Q-site; iron-sulfur; menaquinol Correspondence R. A. Rothery, Department of Biochemistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7 Fax: +1 780 492 0886 Tel: +1 780 492 2229 E-mail: Richard.Rothery@UAlberta.ca (Received 13 September 2004, revised 22 October 2004, accepted 1 November 2004) doi:10.1111/j.1742-4658.2004.4469.x We have used fluorescence quench titrations, EPR spectroscopy and steady-state kinetics to study the effects of site-directed mutants of FrdB, FrdC and FrdD on the proximal menaquinol (MQH 2 ) binding site (Q P )of Escherichia coli fumarate reductase (FrdABCD) in cytoplasmic membrane preparations. Fluorescence quench (FQ) titrations with the fluorophore and MQH 2 analog 2-n-heptyl-4-hydroxyquinoline-N-oxide (HOQNO) indi- cate that the Q P site is defined by residues from FrdB, FrdC and FrdD. In FQ titrations, wild-type FrdABCD binds HOQNO with an apparent K d of 2.5 nm, and the following mutations significantly increase this value: FrdB- T205H (K d ¼ 39 nm); FrdB-V207C (K d ¼ 20 nm); FrdC-E29L (K d ¼ 25 nm); FrdC-W86R (no detectable binding); and FrdD-H80K (K d ¼ 20 nm). In all titrations performed, data were fitted to a monophasic bind- ing equation, indicating that no additional high-affinity HOQNO binding sites exist in FrdABCD. In all cases where HOQNO binding is detectable by FQ titration, it can also be observed by EPR spectroscopy. Steady-state kinetic studies of fumarate-dependent quinol oxidation indicate that there is a correlation between effects on HOQNO binding and effects on the observed K m and k cat values, except in the FrdC-E29L mutant, in which HOQNO binding is observed, but no enzyme turnover is detected. In this case, EPR studies indicate that the lack of activity arises because the enzyme can only remove one electron from reduced MQH 2 , resulting in it being trapped in a form with a bound menasemiquinone radical anion. Overall, the data support a model for FrdABCD in which there is a single redox-active and dissociable Q-site. Abbreviations DmsABC, E. coli dimethylsulfoxide reductase; FQ, fluorescence quench; FrdABCD, E. coli fumarate reductase; FrdCAB, Wolinella succinogenes fumarate reductase; HOQNO, 2-n-heptyl-4-hydroxyquinoline-N-oxide; LPC, oxidized lapachol [2-hydroxy-3-(3-methyl-2-butenyl)- 1,4-naphthoquinone]; LPCH 2 , reduced lapachol; MQ, menaquinone; MQH 2 , menaquinol; NarGHI, nitrate reductase A; SdhCAB, Bacillus subtilis succinate dehydrogenase; SdhCDAB, E. coli and ⁄ or eukaryotic succinate dehydrogenase. FEBS Journal 272 (2005) 313–326 ª 2004 FEBS 313 subunits, FrdC (15 kDa) and FrdD (13.1 kDa). The crystal structure of FrdABCD has been reported at 3.3 A ˚ resolution [3,4], and has an overall architecture similar to that of the E. coli complex II homolog SdhCDAB (succinate:ubiquinone oxidoreductase) [5,6]. Each enzyme contains a single FAD that is covalently bound to the catalytic subunit (FrdA ⁄ SdhA) and three [Fe-S] clusters (a [2Fe-2S] cluster, a [4Fe-4S] cluster, and a [3Fe-4S] cluster) coordinated by the electron- transfer subunit (FrdB ⁄ SdhB) [1]. However, important differences exist between the membrane-intrinsic domains of the two enzymes [1,7]. The membrane- intrinsic domain of SdhCDAB coordinates a single heme b (b 556 ) that is sandwiched between the SdhC and SdhD subunits [8,9]. Quinone binding and reduc- tion is believed to take place in the region between the heme and the [3Fe-4S] cluster of SdhB [1,6]. In the case of FrdABCD, the membrane-intrinsic domain does not contain heme, but instead contains two menaquinones at discreet sites in the crystallized form of the enzyme [3,4]. In both enzymes, despite the available structures, the number of functional quinone ⁄ quinol binding sites has yet to be unequivocally determined. The menaquinones identified in the crystal structure of FrdABCD [3] are located at sites towards the inner (cytoplasmic) and outer (periplasmic) sides of the mem- brane-intrinsic domain of the enzyme (FrdCD). One site, the Q P site (the proximal Q-site), is located in the interface region between the FrdCD subunits and the [3Fe-4S] cluster coordinating region of FrdB on the cytoplasmic side of the membrane. The other site, the Q D site (the distal Q-site) is located approximately 25 A ˚ from the Q P site on the opposite (periplasmic) side of the membrane [3,10]. The relatively large distance between the two sites may preclude direct electron-trans- fer through the protein medium, which is believed to be limited to a distance of approximately 14 A ˚ [11]. How- ever, a third region of electron density has been identi- fied recently between the Q P and Q D sites (the ‘M’ site), and is centered approximately 13 A ˚ from each Q-site [4]. If this electron density corresponds to an additional electron-transferring cofactor, it could provide a conduit for electron-transfer from the Q D site to the Q P site. However, analyses of the bioenergetics of respiratory growth of E. coli on fumarate indicate that FrdABCD turnover does not produce a transmembrane electro- chemical potential [12], suggesting the presence of a sin- gle dissociable and redox-active Q-site that is formally located on the cytoplasmic side of the membrane. Menaquinol (MQH 2 ) oxidation by FrdABCD has been studied using a combination of site-directed muta- genesis, enzymology, EPR spectroscopy and X-ray crys- tallography. Initial mutagenesis studies suggested that there may be two Q-sites present – a polar Q B site (equivalent to the Q P site), and an apolar Q A site (equiv- alent to the Q D site) [13–15]. Investigation of the steady- state kinetics of quinol-dependent fumarate reduction by FrdABCD suggests that MQH 2 binding and oxida- tion occur at a single site [16]. Kinetic studies carried out in the presence of HOQNO or alkylated dinitro- phenol derivatives also support the presence of a single MQH 2 oxidation site [17]. By exploiting the fluorescent properties of HOQNO in fluorescence quench (FQ) titrations, we determined that this inhibitor binds at a single high-affinity site within FrdABCD [18,19]. EPR studies indicate that this high-affinity site is conforma- tionally linked to the [3Fe-4S] cluster of FrdB [18]. The emerging hypothesis that there is a single site for MQH 2 or HOQNO binding has been complicated recently by the observation in crystallographic studies that the Q D site is unoccupied when HOQNO or a dinitrophenol derivative is bound at the Q P site [4]. Given the available structural information on FrdABCD, it would therefore be of interest to examine the effects of a range of site- directed mutants on the HOQNO binding properties and enzymology of the enzyme. In this paper, we evaluate the effects of mutation of amino acid residues located in the vicinity of the Q P site on HOQNO binding to FrdABCD. We have deter- mined the effect of each mutation on HOQNO binding detected by FQ titration and EPR spectroscopy. We have also investigated the effects the mutants have on the steady-state kinetics of fumarate-dependent quinol oxidation. Results Selection of mutants of FrdB, FrdC and FrdD The following residues are located within approximately 5A ˚ of the menaquinone (MQ) observed at the Q P -site in the structure of FrdABCD: T205, F206, Q225 and K228 from FrdB; R28, E29, W86, L89 and A93 from FrdC; and W14, F17, G18, H80, R81 and H84 from FrdD [3,4,10]. Site-directed mutants of some of these res- idues have been generated and partially characterized, including the following: FrdC-E29L [14,20], FrdC- W86R, FrdD-H80K and FrdD-H84K [14]. In the con- text of this study, mutants of the following residues located at a slightly greater distance from the Q P site are also potentially of interest: FrdB-V207 (% 8A ˚ from Q P , a FrdB-V207C mutant) [21], and FrdC-A32 (% 9A ˚ from Q P , a FrdC-A32V mutant) [14]. At an even greater distance away from the Q P site is FrdC-F38 (% 18 A ˚ ), a mutation at this position (FrdC-F38M [14]), would be expected to have little effect on MQH 2 binding and Quinol binding to E. coli fumarate reductase R. A. Rothery et al. 314 FEBS Journal 272 (2005) 313–326 ª 2004 FEBS oxidation. Finally, we generated a mutant of FrdB-T205 (FrdB-T205H) to assess the role of the [3Fe-4S] cluster binding domain of FrdB in defining the Q P -site. This residue is sandwiched between the [3Fe-4S] cluster and the Q P site. All eight mutant enzymes were studied to assess the effects of the mutations on MQH 2 binding using FQ titrations, EPR spectroscopy and steady-state kinetic studies. The locations of all the mutated residues located within % 10 A ˚ of the Q P site are illustrated in Fig. 1. HOQNO has a very similar structure to that of MQ, and as a result appears to bind to the Q P site in an almost identical way (compare Fig. 1A and B with C and D). This similarity in both structure and binding renders HOQNO an excellent inhibitor with which to characterize the Q P site of FrdABCD. FQ titrations of HOQNO binding to mutant FrdABCD HOQNO is a close structural analog of MQH 2 ⁄ MQ and is a very potent inhibitor of FrdABCD [16,18]. When excited at 341 nm, free HOQNO in aqueous solution fluoresces with an emission wavelength of 479 nm. Its fluorescence is completely quenched when bound to FrdABCD and certain other E. coli respirat- ory chain enzymes (including dimethylsulfoxide reduc- tase and nitrate reductase A [18,19,22–24]). This enables its binding to a Q-site to be analyzed by FQ titration. Figure 2 shows representative titrations of membranes containing the wild-type and mutant enzymes studied herein. Data for all of the mutants is presented in Table 1. DW35 membranes lacking FrdABCD (Fig. 2A) do not exhibit high-affinity HOQNO binding. The following FrdABCD mutants bind HOQNO with K d values equivalent to that of the wild-type enzyme (K d ¼ 2.5 nm; Fig. 2B): FrdC-A32V (2.5 nm; not shown), FrdC-F38M (2.5 nm; not shown) and FrdD-H84K (3.0 nm, not shown). At the opposite extreme, it is clear that the FrdC-W86R mutant does not exhibit high-affinity HOQNO binding (Fig. 2E). This mutant appears to have a similar phenotype to that of the previously reported FrdC-H82R mutant [18,25]. Intermediate effects are observed with the fol- lowing mutants: FrdB-T205H (K d ¼ 39 nm; Fig. 2C), FrdB-V207C (20 nm; not shown), FrdC-E29L (25 nm; Fig. 2D) and FrdD-H80K (20 nm; Fig. 2F). Based on Fig. 1. Positions of the mutated residues close to the Q P site studied herein. A and B show views of the MQ-bound form of FrdA- BCD (1L0V), whereas C and D show views of the HOQNO-bound form (1KF6). A and C represent views from an identical perspec- tive, as do panels B and D (Experimental procedures). (A) Looking along the axis defi- ned by the two keto-oxygens of the prox- imal menaquinone (MQ) naphthoquinone bicycle. (B) Looking along the axis of the MQ towards the isoprenoid chain. (C) The same perspective as A, but with HOQNO bound. (D) The same perspective as B, but with HOQNO bound. In all panels, FrdB and FrdA are above the MQ ⁄ HOQNO plane, and FrdC and FrdD are substantially below the MQ ⁄ HOQNO plane. Residues from FrdB, FrdC and FrdD have labels starting with ‘B-’, ‘C-’, and ‘D-’, respectively. R. A. Rothery et al. Quinol binding to E. coli fumarate reductase FEBS Journal 272 (2005) 313–326 ª 2004 FEBS 315 these observations and the FrdABCD structure [3,4], it is clear that residues from FrdB, FrdC and FrdD play important roles in defining the Q P site. In every case where binding is detected, the data can be fitted to an equation (Eqn 1) describing noncooperative binding at a single site within FrdABCD. Table 1 shows the calculated specific concentration of HOQNO binding sites for each mutant in which binding is detected by FQ titration. It also shows the concentration of FrdABCD calculated by EPR spin quantitation of both the [2Fe-2S] and [3Fe-4S] clusters. In each case, the estimated number of Q-sites per enzyme is very close to unity, indicating that HOQNO binding occurs at a single site within FrdABCD. Based on enzymes that bind HOQNO, 1.02 ± 0.12 sites were observed per [3Fe-4S] cluster and 1.05 ± 0.09 sites were observed per [2Fe-2S] cluster. Detection of HOQNO binding by EPR spectroscopy Figure 3 shows the effect of HOQNO on the EPR spectrum around g ¼ 2.0 of ferricyanide-oxidized HB101 membrane samples containing wild-type and mutant FrdABCD. EPR spectra of membranes lacking overexpressed FrdABCD exhibit low-intensity features around g ¼ 2.0 upon which HOQNO has little effect (Fig. 3A). Spectra of membranes containing over- expressed wild-type FrdABCD exhibit the EPR spec- trum of its oxidized [3Fe-4S] cluster (Fig. 3B). This spectrum is nearly isotropic with a peak at g ¼ 2.02 (g z ) and a broad trough immediately up-field. As has been reported previously [18,20], addition of HOQNO elicits the observation of an additional peak-trough at approximately g ¼ 1.98 (g xy ). Both of the FrdB mutants studied herein (FrdB- T205H and FrdB-V207C) have significant effects on the EPR properties of FrdABCD. In the case of the FrdB-T205H mutant, the [3Fe-4S] cluster line-shape is narrower than that of the wild-type (note the position of the trough in the spectrum without HOQNO; Fig. 3C). As is the case for the wild-type enzyme, addi- tion of HOQNO results in the resolution of a peak- trough on the high-field side of the g ¼ 2.02 peak. This peak-trough is centered at a g-value reflecting the narrower spectrum of the [3Fe-4S] cluster in the Fig. 2. Representative fluorescence quench titrations of HOQNO binding to wild-type and mutant FrdABCD in DW35 membranes. Titrations were carried out using membranes from E. coli DW35 transformed with plasmids encoding wild-type and mutant FrdABCD at total mem- brane protein concentrations of 0.2 (e), 0.3 (h), 0.4 (n), and 0.5 mgÆmL )1 (s). Data were fitted to the following specific enzyme concentra- tions (nmolÆ mg protein )1 )andK d values (nM): (A) background, 0.36, > 500; (B) wild-type, 3.54, 2.5; (C) FrdB-T205H, 3.13, 39; (D) FrdC-E29L, 3.26, 25; (E) FrdC-W86R, negligible binding; (F) FrdD-H80K, 3.61, 20. Note that in the cases of the background and FrdC-W86R mutant membranes, the data presented represent insignificant binding. Quinol binding to E. coli fumarate reductase R. A. Rothery et al. 316 FEBS Journal 272 (2005) 313–326 ª 2004 FEBS FrdB-T205H mutant in the absence of inhibitor (g xy ¼ 2.0 in the presence of inhibitor rather than at 1.98). Figure 3D shows the spectrum of oxidized mem- branes containing overexpressed FrdB-V207C mutant enzyme. In agreement with Manadori et al. [21], little or no [3Fe-4S] cluster is assembled into this mutant enzyme (compare Fig. 3A and D), and therefore HOQNO binding cannot be detected by its perturba- tion of the EPR spectrum of the oxidized enzyme (see below). In contrast to the results of Ha ¨ gerha ¨ ll et al. [20], the EPR experiments reported herein indicate that HO- QNO elicits an effect on the EPR line-shape of the [3Fe-4S] cluster of the FrdC-E29L mutant enzyme (Fig. 3E). This result is consistent with the observation of HOQNO binding by FQ titration (Fig. 2D and Table 1). For the other mutations located within the membrane anchor subunits (FrdC and FrdD), there is a strong correlation between the observation of an HOQNO-induced line-shape change and the observa- tion of inhibitor binding in FQ titrations (compare Figs 2 and 3, Table 1). Thus, no EPR line-shape change is elicited on the FrdC-W86R mutant [3Fe-4S] cluster spectrum (Fig. 3G). HOQNO binding to reduced wild-type and FrdC-V207C mutant enzyme The EPR properties of reduced wild-type FrdABCD are complicated by spin–spin interactions between the paramagnetic [Fe-S] clusters present (viz. between the S ¼ ½ [2Fe-2S] and [4Fe-4S] clusters and the S ¼ 2 reduced [3Fe-4S] cluster) [26]. The clusters have mid- point potentials (E m values) of % )79 mV ([2Fe-2S] c1uster [27]), )320 mV ([4Fe-4S] c1uster [26]), and )70 mV ([3Fe-4S] c1uster [18,21,26]). Because of the pairing of the [3Fe-4S] cluster with the [4Fe-4S] cluster in a 7Fe ferredoxin-type motif, we examined the possi- bility that HOQNO binding to the Q P site may affect the EPR properties of the fully reduced enzyme. Figure 4A shows that HOQNO has no effect on the spectrum of dithionite-reduced HB101 membranes lacking overexpressed FrdABCD. No differences are observed between the spectrum recorded in the absence of HOQNO (Fig. 4Ai) and that recorded in its pres- ence (Fig. 4Aii). The spectrum of reduced membranes containing overexpressed wild-type FrdABCD recor- ded in the absence of HOQNO has an intense peak at g ¼ 2.02 (g z ) and a peak-trough at g ¼ 1.93 (g xy ) (Fig. 4Bi). These comprise the EPR spectrum of the [2Fe-2S] cluster of FrdB [27]. The EPR spectrum of the [4Fe-4S] cluster manifests itself as a very broad, rapidly relaxing signal underlying that of the [2Fe-4S] cluster [21,26] with peaks at g ¼ 2.18 and troughs at g ¼ 1.82 and g ¼ 1.66. No significant effect is elicited on this spectrum by HOQNO (compare Fig. 4Bi and Bii). Figure 4C shows similar spectra recorded of mem- branes containing the overexpressed FrdB-V207C mutant that contains a [4Fe-4S] cluster in place of the [3Fe-4S] cluster of the wild-type enzyme [21]. In this case, the broad underlying spectrum arises from the Table 1. Effect of the FrdABCD mutations on HOQNO binding determined by FQ titrations and EPR spectroscopy in E. coli strain DW35. The concentration of the dithionite-reduced [2Fe-2S] cluster was estimated by double integration of EPR spectra recorded at 40 K under nonsaturating conditions using a CuEDTA concentration standard [47]. The concentration of the ferricyanide-oxidized [3Fe-4S] cluster was estimated by double integration of EPR spectra recorded at 9 K under nonsaturating conditions using a Cu-EDTA concentration standard [47]. The effect of HOQNO on the [3Fe-4S] cluster EPR line-shape was determined using E. coli HB101 membranes. Samples and EPR con- ditions were as described for Figs 3 and 4. ND, not detected. Membrane preparation HOQNO K d (nM) [Q-sites] (nmolÆmg )1 ) by FQ [2Fe-2S] (nmolÆmg )1 ) by EPR [3Fe-4S] (nmolÆmg )1 ) by EPR Q-sites per [2Fe-2S] Q-sites per [3Fe-4S] EPR effect Background ND ND ND a ND a ND ND No FrdABCD 2.5 3.54 3.48 3.60 1.02 0.98 Yes FrdB-T205H 39.0 3.13 3.21 2.49 0.98 1.26 Yes FrdB-V207C 20.0 1.44 1.39 0.16 1.04 ND b Yes c FrdC-E29L 25.0 3.26 2.74 3.11 1.19 1.05 Yes FrdC-A32V 2.5 2.97 2.96 3.16 1.00 0.94 Yes FrdC-F38M 2.5 3.26 3.14 3.44 1.04 0.95 Yes FrdC-W86R ND ND 2.37 2.34 ND ND No FrdD-H80K 20.0 3.61 3.15 3.47 1.15 1.04 Yes FrdD-H84K 3.0 3.68 3.09 3.47 1.19 1.06 Yes a Features clearly attributable to either a [2Fe-2S] cluster or a [3Fe-4S] are not detected in spectra of reduced and oxidized membrane sam- ples from E. coli strain DW35. b The FrdB-V207C mutant contains a [4Fe-4S] cluster in place of the [3Fe-4S] cluster of the wild-type enzyme. c In this case, the effect of HOQNO was determined by analyses of spectra of dithionite-reduced samples recorded as described in the legend to Fig. 4. R. A. Rothery et al. Quinol binding to E. coli fumarate reductase FEBS Journal 272 (2005) 313–326 ª 2004 FEBS 317 spin-coupled pair of [4Fe-4S] clusters and comprises a peak at g ¼ 2.29, and troughs at g ¼ 1.87 and 1.67. Addition of HOQNO causes the appearance of a peak at g ¼ 1.98 (compare Figure 4Ci and ii). Overall, these data are consistent with there being a perturbation of the engineered [4Fe-4S] cluster in the FrdB-V207C mutant by HOQNO, and with there being no pertur- bation of the [4Fe-4S] cluster of the wild-type enzyme. Fig. 4. Effect of HOQNO on the engineered [4Fe-4S] cluster EPR spectrum of FrdB-V207C FrdABCD in HB101 membranes. Mem- branes were incubated in the absence of (i) or presence of (ii) 0.5 m M HOQNO for 5 min, then reduced with 5 mM dithionite under argon for 5 min prior to being frozen in liquid nitrogen. Spec- tra are presented of membranes containing no overexpressed enzyme (A), and membranes containing overexpressed wild-type (B), and FrdB-V207C (C). EPR spectra were recorded as described for Fig. 3. Fig. 3. Effect of HOQNO on the [3Fe-4S] cluster EPR spectrum of wild-type and mutant FrdABCD in HB101 membranes. Membranes were incubated with 0.5 m M HOQNO (thick lines) or an equivalent volume of ethanol for 5 min (thin lines), then oxidized with 0.2 m M ferricyanide for two minutes prior to being frozen in liquid nitrogen. Spectra are shown of membranes containing no overexpressed enzyme (A), and membranes containing overexpressed wild-type (B), FrdB-T205H (C), FrdB-V207C (D), FrdC-E29L (E), FrdC-A32V (F), FrdC-W86R (G), and FrdD-H80K (H). EPR spectra were recorded under the following conditions: temperature, 12 K; microwave power, 20 mW at 9.47 GHz; modulation amplitude, 10 G pp at 100 KHz. Spectra were normalized to a nominal protein concentration of 30 mgÆmL )1 . In addition, the absolute intensity of the g ¼ 2.02 peaks were normalized for each pair of spectra. Quinol binding to E. coli fumarate reductase R. A. Rothery et al. 318 FEBS Journal 272 (2005) 313–326 ª 2004 FEBS Effect of the mutations on the quinol:fumarate oxidoreductase activity of FrdABCD In order to gain a broader understanding of the effects of the mutants on the physiological quinol oxidation reaction catalyzed by FrdABCD, we studied their effects on the steady-state kinetics of the quinol: fumarate oxidoreductase reaction using the MQH 2 analog lapachol [2-hydroxy-3-(3-methyl-2-butenyl)-1,4- naphthoquinone; LPC]. When reduced, this substrate (LPCH 2 ) has significant structural similarity to MQH 2 , and in its oxidized form has a convenient absorbance peak in the visible region at 481 nm in aqueous solu- tion [16]. Figure 5 shows representative Eadie–Hofstee plots describing the steady-state kinetic behavior of wild-type and a subset of the mutants of FrdABCD in DW35 membranes. The wild-type enzyme has a K m for LPCH 2 of approximately 225 lm and a k cat of approximately 71 s )1 . The FrdB-T205H and FrdD- H80K mutants have increased K m values (of 355 lm and 670 lm, respectively), but have similar k cat values to that of the wild-type (68 s )1 and 67 s )1 , respect- ively). The FrdC-A32V mutant exhibits quite different behavior, with a decrease observed in both the K m and the k cat values (to 115 lm and 31 s )1 , respectively). Likewise, the FrdB-V207C mutant also displayed a decrease in both K m and k cat (Table 2). Despite the HOQNO binding observed both by EPR and FQ titra- tion, the FrdC-E29L mutant exhibited no quinol:fuma- rate oxidoreductase activity. Kinetic data for all of the mutants are summarized in Table 2. Detection of a menasemiquinone radical anion in the FrdC-E29L mutant The FrdC-E29L mutant is unusual because it retains high-affinity HOQNO binding (Table 1 and Fig. 2), but demonstrates no fumarate-dependent LPCH 2 oxi- dation. It has been demonstrated previously by redox potentiometry to stabilize a menasemiquinone radical Fig. 5. Determination of steady-state kinetic parameters for wild- type and mutant FrdABCD. e, wild-type, K m ¼ 225 lM, k cat ¼ 71 s )1 . h, FrdAB T205H CD; K m ¼ 355 lM, k cat ¼ 68 s )1 . s, FrdABCD H80K , K m ¼ 670 lM, k cat ¼ 67 s )1 . n, FrdABC A32V C, K m ¼ 115 l M, k cat ¼ 31 s )1 . Assays at a range of LPCH 2 concentra- tions were carried out as described in the Experimental proce- dures. Table 2. Effect of the FrdABCD mutants on the kinetic parameters for lapachol oxidation in E. coli strain DW35. Growth, ability of the DW35 based strains used herein to support anaerobic growth using glycerol as carbon source and fumarate as respiratory oxidant. HOQNO binding is as judged by the data presented in Table 1. Group, classification of mutant phenotypes: 0, no quinol oxidation, no high-affinity HOQNO binding, does not support growth; 1, normal or modulated K m and normal k cat for quinol oxidation, high-affinity HOQNO binding, supports growth; 2 ) normal or modulated K m with decreased k cat , high-affinity HOQNO binding, supports growth; 3, no quinol oxidation, high-affinity HOQNO binding, does not support growth. NA, not applicable. Membranes from the background strain, E. coli DW35, do not contain FrdABCD. ND, not detected. Membrane preparation K m a (lM) k cat a (s )1 ) Growth on GF HOQNO Binding Group Background ND ND No No NA FrdABCD 225 ± 25 71 ± 3 Yes Yes 1 FrdB-T205H 355 ± 34 68 ± 4 Yes Yes 1 FrdB-V207C 203 ± 17 31 ± 1 Yes Yes 2 FrdC-E29L ND ND No Yes 3 FrdC-A32V 115 ± 6 31 ± 1 Yes Yes 2 FrdC-F38M 385 ± 40 82 ± 5 Yes Yes 1 FrdC-W86R ND ND No No 0 FrdD-H80K 670 ± 47 67 ± 3 Yes Yes 1 FrdD-H84K 451 ± 34 75 ± 3 Yes Yes 1 a Kinetic parameters were determined from Eadie–Hofstee plots such as those presented in Fig. 5. R. A. Rothery et al. Quinol binding to E. coli fumarate reductase FEBS Journal 272 (2005) 313–326 ª 2004 FEBS 319 anion [20]. Thus, a plausible explanation for the lack of quinol:fumarate oxidoreductase activity is that this mutant becomes trapped in a state in which a mena- semiquinone radical anion is bound to the Q P site. We tested this hypothesis by attempting to observe turn- over-induced radical species in the wild-type and FrdC-E29L mutant enzymes. Figure 6 shows EPR spectra recorded at 150K of variously treated mem- brane preparations. No g ¼ 2.00 radical signal is detected in oxidized and dithionite-reduced mem- branes containing overexpressed wild-type enzyme (Fig. 6A,B). Addition of fumarate to dithionite- reduced membranes containing wild-type enzyme elicits the observation of a small g ¼ 2.006 signal consistent with the appearance of a menasemiquinone radical intermediate under turnover conditions. As is the case for the wild-type enzyme, dithionite-reduced mem- branes containing the FrdC-E29L mutant enzyme exhi- bit no radical signal. A significant signal is observed in oxidized membranes containing mutant enzyme. An intense g ¼ 2.006 signal is observed when the FrdC- E29L mutant enzyme is reduced with dithionite and then oxidized with fumarate, consistent with this mutant becoming trapped in a menasemiquinone bound form when enzyme turnover is attempted (Fig. 6G,H). Discussion We have investigated the effects of a number of point mutations on the affinity of FrdABCD for HOQNO. In each case where HOQNO binding is detected, there is a striking correlation between the concentration of binding sites and the concentration of enzyme deter- mined by EPR spin quantitation of the [2Fe-2S] and [3Fe-4S] clusters (Table 1). Where modulation of the K d for HOQNO is detected, the FQ data can be fitted to a binding equation describing noncooperative bind- ing at a single site within FrdABCD. These observa- tions are consistent with the presence of a single redox-active dissociable Q-site in FrdABCD, and indi- cate that this site coincides with the Q P site observed in the crystal structures of Iverson et al. [3,4]. The HOQNO binding data agree with the structure of FrdABCD incubated in the presence of HOQNO, in which the inhibitor is bound exclusively at the Q P site. We previously reported the effect of HOQNO on the EPR line-shape of the [3Fe-4S] cluster of FrdB, and showed that a point mutation in FrdC, FrdC- H82R, eliminated both this effect and HOQNO bind- ing detected by FQ titration [18]. However, the posi- tion of FrdC-H82 within the hydrophobic core of FrdC (> 5 A ˚ away from Q P ), along with the relatively severe Arg substitution, warranted re-examination of HOQNO binding to FrdABCD using a range of avail- able mutations. It is quite possible that the FrdC- H82R mutation causes relatively gross conformational changes that could affect both the Q P and Q D sites. While some of the mutations studied herein may fall into the same category as the FrdC-H82R mutant (i.e. Fig. 6. Demonstration that turnover of the FrdC-E29L mutant is stalled with a menasemiquinone radical-bound form in E. coli DW35 membranes. EPR spectra were recorded of DW35 mem- branes containing wild-type enzyme (A–D) and FrdC-E29L mutant enzyme (E–H). (A, E), membranes reduced with 5 m M dithionite for 2 min; (B) and (F), oxidized membranes. (C) and (G), membranes reduced with dithionite for 2 min, then treated with 25 m M fuma- rate for 30 s. (D) and (H), as for (C) and (G), but with the incubation with fumarate for 1 min. EPR spectra were recorded at 150 K using a microwave power of 20 mW at 9.44 GHz and a modulation ampli- tude of 1.2 G pp . Spectra were normalized to a protein concentration of 30 mgÆmL )1 . Quinol binding to E. coli fumarate reductase R. A. Rothery et al. 320 FEBS Journal 272 (2005) 313–326 ª 2004 FEBS the FrdC-W86R mutant), we were able to study a range of mutations that are more likely to have local effects within the protein. Overall, there is a good cor- relation between the location of the mutated residues and the severity of the observed effects on HOQNO binding (compare Figure 1 and Table 1). An effect on the EPR spectrum of the [3Fe-4S] clus- ter is clearly observed in each case where HOQNO binding is detected by FQ titration. In addition, we were able to observe that this effect is not propagated beyond the location of the [3Fe-4S] cluster (Fig. 4). The FrdB-V207C mutant contains a [4Fe-4S] cluster in place of the [3Fe-4S] cluster of the wild-type enzyme, so that the mutant enzyme contains two [4Fe-4S] clus- ters coordinated by a motif similar to those found in the bacterial 8Fe ferredoxins [21]. In this mutant, the converted cluster is paramagnetic in its reduced state, but its spectroscopic analysis is complicated by spin– spin interactions with the other two reduced clusters of the enzyme (Fig. 4). Despite this, we were able to dem- onstrate that HOQNO elicits a line-shape change on the EPR spectrum of the fully reduced FrdB-V207C mutant. Overall, the combination of FQ and EPR data confirm that the Q P site is defined by residues from FrdB, FrdC and FrdD. Our observation that the Q P site is closely coupled to the [3Fe-4S] cluster of FrdB bears interesting com- parison with data reported for the membrane-bound E. coli dimethylsulfoxide reductase (DmsABC). This enzyme is a complex iron–sulfur molybdoenzyme that, like FrdABCD, contains no heme within its mem- brane anchor domain (DmsC) [28]. The electron transfer subunit of DmsABC (DmsB) contains four [4Fe-4S] clusters, and one of these can be changed to a [3Fe-4S] cluster by site-directed mutagenesis (in a DmsB-C102S mutant) [29]. Treatment of this mutant with HOQNO results in a perturbation of the [3Fe-4S] cluster EPR spectrum that is similar to that reported for the [3Fe-4S] cluster of FrdABCD [18,30]. It is therefore likely that the dissociable Q-site of DmsABC is located in the interface region between the membrane-anchor (DmsC) and the electron-trans- fer subunit (DmsB). Comparison of the FQ titration, EPR and steady- state kinetic data on the FrdABCD mutants reported herein supports their assignments to the following groups: 0 – no enzyme activity, no high-affinity HOQNO binding, unable to support growth. Members: the FrdC-W86R mutant and the FrdC-H82R mutant pre- viously reported by us [18,25]. 1 – normal or modulated K m , normal k cat , high-affinity HQONO binding, able to support growth. Members: the wild-type enzyme, the FrdB-T205H, FrdC-F38M, FrdD-H80K and FrdD-H84K mutants. 2 – normal or modulated K m , decreased k cat , high- affinity HOQNO binding, able to support growth. Members: the FrdB-V207C and FrdC-A32V mutants. 3 – no quinol oxidation, high-affinity HOQNO bind- ing, unable to support growth. Member: the FrdC- E29L mutant. Overall, the kinetic data presented herein are consis- tent with the occurrence of simple Michaelis–Menten kinetics, with LCPH 2 binding and oxidation occurring at a single Q-site (Fig. 5). However, it is notable that mutants that appear to have little effect on HOQNO binding can modulate the observed steady-state kinet- ics of the enzyme. For example, the FrdC-A32V mutant significantly decreases the observed k cat .A possible explanation for this is that the increased bulk of the hydrophobic sidechain is able to stabilize qui- nol ⁄ quinone species at the Q P site, decreasing the rate of substrate entry and product egress. The other mutant with a significantly decreased k cat , the FrdB- V207C mutant contains a low potential [4Fe-4S] clus- ter (E m of % )370 mV [21] in place of the native [3Fe-4S] cluster with an E m of % )70 mV). In this case, it is likely that the relative inefficiency of the low- potential [4Fe-4S] cluster in accepting electrons from reduced quinol explains the decreased k cat . The two FrdD mutants studied herein produced somewhat unexpected results: both are HisfiLys resi- due changes (FrdD-H80 and FrdD-H84), yet only the FrdD-H80K mutant has a significant effect on both the K d for HOQNO and the K m for LPCH 2 . Careful examination of the structure of FrdABCD (PDB file L0V [4], Fig. 1) reveals a possible explanation for this. Whilst the sidechain of FrdD-H84 is marginally closer to the MQ at the Q P site than that of FrdD-H80, the axis of the His-84 imidazole points slightly away from the MQ naphthoquinone bicycle, whereas that of the His-80 imidazole appears to be pointing at least parti- ally towards it. Thus, it is more likely that the side- chain of the Lys substitution of FrdD-H80 elicits an effect on HOQNO binding and LPCH 2 oxidation than the Lys substitution of FrdD-H84. Although this explanation appears plausible, it should be noted that it is based on structural data of fairly low resolution (3.3 A ˚ ) [3,4]. The FrdB-T205H mutant is of interest in establish- ing the role of FrdB in defining the Q P site. As men- tioned previously (Results), this mutation was chosen because of the location of FrdB-T205H with respect to the Q P site, the [3Fe-4S] cluster and the interface between FrdB and the membrane anchor subunits. With the exception of the FrdC-W86R mutant, the R. A. Rothery et al. Quinol binding to E. coli fumarate reductase FEBS Journal 272 (2005) 313–326 ª 2004 FEBS 321 FrdB-T205H mutant has the largest effect on the K d for HOQNO, raising it from % 2.5 nm to 39 nm (Fig. 2 and Table 1). In addition to its effect on HOQNO binding, this mutant is also of interest for the follow- ing reasons: (a) it has a subtle effect on the [3Fe-4S] cluster EPR line-shape of both the untreated and HO- QNO treated enzyme (the linewidth is significantly nar- rowed, compare Fig. 3B and C) and (b) it changes the sequence of the [3Fe-4S] cluster-coordinating Cys group so that it contains the critical His residue that is present after the first Cys in the carboxin-sensitive complex II enzymes [31]. We are currently investi- gating the effect of this mutation on the carboxin-sen- sitivity of FrdABCD (E Maklashina, RA Rothery, JH Weiner and G Cecchini, unpublished data). Of the mutants classified above, the single member of the Class 3 subgroup is particularly interesting. The FrdC-E29L mutant has no quinol:fumarate oxidoreduc- tase activity, yet it retains HOQNO binding measured by both the FQ and EPR methods (Figs 2 and 3). Ha ¨ gerha ¨ ll and coworkers [20] demonstrated by potenti- ometric titration and EPR spectroscopy that a mena- semiquinone radical anion is stabilized in this mutant. Examination of FrdABCD structure reveals that the position of FrdC-E29 is suitable for it to act as a proton acceptor during enzyme turnover [3,4]. Furthermore, it is widely believed that HOQNO represents a good ana- log of the menasemiquinone radical intermediate [32,33]. Our observation of a radical when enzyme turn- over is attempted indicates that the mutant is only able to accept a single electron from MQH 2 , resulting in a bound and stabilized menasemiquinone intermediate, thus explaining the observed binding of HOQNO and the lack of quinol:fumarate oxidoreductase activity. In addition to the E. coli complex II homologs (FrdABCD and SdhCDAB), a high-resolution struc- ture is available for one additional bacterial complex II homolog. This is the Wolinella succinogenes fuma- rate reductase (FrdCAB) [34,35] which belongs to a distinct class of complex II homologs that includes the Bacillus subtilis succinate dehydrogenase (SdhCAB) [33]. These enzymes have a single membrane anchor subunit (FrdC and SdhC, respectively) that contains two hemes. The structure of the W. succinogenes Frd- CAB [35] reveals that one heme is proximal to the membrane-extrinsic dimer (heme b P ), whilst the other is distal to it (heme b D ). It has been demonstrated that a point mutation (FrdC-E66Q) that eliminates MQH 2 oxidation by FrdCAB is located at a site (a Q D site) in close proximity to heme b D towards the periplasmic side of FrdC [34]. In B. subtilis SdhCAB, the heme b D is essential for electron-transfer to MQ [36], and this heme is the only one that appears to be affected by HOQNO [32]. Thus, in contrast to the case in E. coli FrdABCD, in W. succinogenes FrdCAB and B. subtilis SdhCAB, available evidence points towards a model for quinone ⁄ quinol binding in which the redox-active dissociable Q-site is located towards the periplasmic side of the membrane anchor domain (at a Q D site), and that electron-transfer across the membrane to ⁄ from the catalytic dimer is mediated by the two hemes in a manner similar to that observed in E. coli nitrate reductase A (NarGHI) [24,37–40] and suggested for formate dehydrogenase N [41]. The role of the Q D site in FrdABCD remains unre- solved. The data presented herein suggest a model for the enzyme in which quinol binding and oxidation occur exclusively at the Q P site. This is supported by theoretical models of through-protein electron transfer which indicate that the 25 A ˚ distance between the Q P and Q D menaquinones identified in the protein struc- ture is too far to allow for physiologically relevant electron transfer between these sites [11]. Our prelimin- ary investigations of mutants (such as FrdD-F57V and FrdC-V35A) surrounding the MQ D observed in the protein structure indicate that these have no effect on the HOQNO binding detected by FQ titration and by EPR; and have little effect on quinol:fumarate oxidore- ductase activities. A full description of these mutants will appear in a later communication (E Maklashina, RA Rothery, JH Weiner and G Cecchini, unpublished data). Thus, it is likely that the Q D site plays no direct role in menaquinol oxidation. Overall, by using a range of FrdB, FrdC, and FrdD mutants, we have demonstrated that in every case where HOQNO binding is detected, it occurs at a sin- gle site within FrdABCD. In agreement with the struc- tural data of Iverson and coworkers [3,4], we provide biochemical and biophysical evidence for the location of the dissociable and redox-active Q site of FrdABCD being in the interface region between the FrdCD mem- brane-intrinsic domain and the FrdB electron-transfer subunit. These studies provide important information on the mechanism of MQH 2 oxidation by FrdABCD. Experimental procedures Bacterial strains and plasmids E. coli DW35 (zjd::Tn10D(frdABCD)18 sdhC::Kan araD139 D(argF-lac)U169 rpsL150 relA1 flbB5301 deoC1 pfsF25 rbsR [14] does not express FrdABCD or SdhCDAB. E. coli HB101 (supE44 hsdS20 (r B – m B – ) recA13 ara-14 proA2 lacY1 galK2 rpsL20 xyl-5 mtl-1) is a wild-type strain that expres- ses plasmid-encoded FrdABCD to very high levels and generates more consistent EPR data than that obtained Quinol binding to E. coli fumarate reductase R. A. 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(1998) Hydroxylated naphthoquinones as substrates for Escherichia coli anaerobic reductases Biochem J 332, 35–41 17 Maklashina E & Cecchini G (1999) Comparison of catalytic activity and inhibitors of quinone reactions of succinate dehydrogenase (Succinate-ubiquinone oxidoreductase) and fumarate reductase (Menaquinolfumarate oxidoreductase) from Escherichia coli Arch Biochem Biophys 369, 223–232 FEBS Journal... harvested by centrifugation at 10 000 g for 15 min at 4 °C, washed in a buffer containing 100 mm Mops ⁄ KOH and 5 mm EDTA (pH 7.0), and were flash frozen in liquid nitrogen prior to being stored at )70 °C ð1Þ ð3Þ and These equations are from reference [45] The specific fluorescences of the bound and free inhibitor are fbound and ffree, respectively [Itot], [Ibound] and [Ifree] are the concentrations of total,... inactivation of fumarate reductase from Escherichia coli by mutation of the [3Fe-4S]-quinone binding domain J Bacteriol 177, 4587–4592 45 Okun JG, Lummen P & Brandt U (1999) Three classes ¨ of inhibitors share a common binding domain in mitochondrial complex I (NADH:ubiquinone oxidoreductase) J Biol Chem 274, 2626–2630 46 Brandt U & von Jagow G (1991) Analysis of inhibitor binding to the mitochondrial... treatment(s), samples were frozen rapidly in liquid nitrogen-chilled ethanol and were stored under liquid nitrogen prior to EPR characterization To investigate the effect of HOQNO on the EPR line-shape of the [3Fe-4S] cluster, 500 lL membrane samples at % 30 mgÆmL)1 were incubated in the pres- 323 Quinol binding to E coli fumarate reductase ence of 0.5 mm HOQNO for 5 min before being oxidized with 0.2 mm ferricyanide... [16,18] The appearance of oxidized lapachol (LPC) in the assay mixture was followed at 481 nm using a standard laboratory spectrophotometer For each membrane preparation, Km and kcat were determined by generating Eadie–Hofstee plots (v vs v ⁄ s), and the protein concentration was between 0.016 mgÆmL)1 and 0.056 mgÆmL)1 324 R A Rothery et al Structural alignment and molecular graphics Protein structures of . Defining the Q P -site of Escherichia coli fumarate reductase by site-directed mutagenesis, fluorescence quench titrations and EPR spectroscopy Richard. fluorescence quench titrations, EPR spectroscopy and steady-state kinetics to study the effects of site-directed mutants of FrdB, FrdC and FrdD on the proximal