Originally published In Press as doi:10.1074/jbc.M301122200 on March 20, 2003
J. Biol. Chem., Vol. 278, Issue 22, 20245-20258, May 30, 2003
Importance of Conserved N-domain Residues Thr441, Glu442, Lys515, Arg560, and Leu562 of Sarcoplasmic Reticulum Ca2+-ATPase for MgATP Binding and Subsequent Catalytic Steps
PLASTICITY OF THE NUCLEOTIDE-BINDING SITE*
Johannes D. Clausen
,
David B. McIntosh
¶,
Bente Vilsen
,
David G. Woolley
and
Jens Peter Andersen
||
From the
Department of Physiology, University of Aarhus, DK-8000 Aarhus C, Denmark and the
Division of Chemical Pathology, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
Received for publication, February 3, 2003
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ABSTRACT
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Nine single mutations were introduced to amino acid residues Thr441, Glu442, Lys515, Arg560, Cys561, and Leu562 located in the nucleotide-binding domain of sarcoplasmic reticulum Ca2+-ATPase, and the functional consequences were studied in a direct nucleotide binding assay, as well as by steady-state and transient kinetic measurements of the overall and partial reactions of the transport cycle. Some partial reaction steps were also examined in mutants with alterations to Phe487, Arg489, and Lys492. The results implicate all these residues, except Cys561, in high affinity nucleotide binding at the substrate site. Mutations Thr441
Ala, Glu442
Ala, and Leu562
Phe were more detrimental to MgATP binding than to ATP binding, thus pointing to a role for these residues in the binding of Mg2+ or to a difference between the interactions with MgATP and ATP. Subsequent catalytic steps were also selectively affected by the mutations, showing the involvement of the nucleotide-binding domain in these reactions. Mutation of Arg560 inhibited phosphoryl transfer but enhanced the E1PCa2
E2P conformational transition, whereas mutations Thr441
Ala, Glu442
Ala, Lys492
Leu, and Lys515
Ala inhibited the E1PCa2
E2P transition. Hydrolysis of the E2P phosphoenzyme intermediate was enhanced in Glu442
Ala, Lys492
Leu, Lys515
Ala, and Arg560
Glu. None of the mutations affected the low affinity activation by nucleotide of the phosphoenzyme-processing steps, indicating that modulatory nucleotide interacts differently from substrate nucleotide. Mutation Glu442
Ala greatly enhanced reaction of Lys515 with fluorescein isothiocyanate, indicating that the two residues form a salt link in the native protein.
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INTRODUCTION
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The sarcoplasmic reticulum Ca2+-ATPase1 is an energy-transducing enzyme responsible for active transport of Ca2+ from the cytosol into the lumen of sarcoplasmic reticulum. It is an integral 110-kDa membrane protein belonging to the family of P-type ATPases, in which autophosphorylation by ATP of a conserved aspartic acid residue is coupled to conformational changes resulting in ion translocation (Scheme 1). The high resolution x-ray structure of the Ca2+-ATPase crystallized in a Ca2+-bound dephospho form (presumably corresponding to E1Ca2 in Scheme 1) has revealed that the enzyme is made up of 10 membrane-spanning helices and a large cytoplasmic head that binds ATP and catalyzes its hydrolysis to yield ADP and Pi. The head consists of three well defined domains: the nucleotide-binding domain ("domain N," supposed to bind the adenosine part of ATP), phosphorylation domain ("domain P" with Asp351, which is phosphorylated), and actuator domain ("domain A," believed to undergo large movements during the reaction cycle) (1). The catalytic site may, at different stages of the transport cycle, consist of residues contributed from all three head domains, and many questions regarding the nature of the nucleotide-binding site(s) are unresolved.

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SCHEME 1. Ca2+-ATPase reaction cycle. Major conformational changes and ligand binding and dissociation steps are shown. Boxed ATP indicates steps for which the rate is enhanced by additional binding of ATP or MgATP that is not hydrolyzed ("modulatory ATP").
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In domain N, labeling of Lys515 with FITC (2, 3) or Lys492 with TNP-8N3-ATP (4) is competitive with respect to ATP binding at the catalytic site. The specific photolabeling of Lys492 with TNP-8N3-ATP has permitted measurement of the binding of nucleotide to mutant Ca2+-ATPases in a competition assay and identified Phe487, Arg489, and Lys492 as likely nucleotide-binding residues (5). The location of TNP-AMP in the crystal structure, obtained from a difference Fourier map following soaking of the E1Ca2 crystals in a solution containing TNP-AMP, supported involvement of these residues in the binding of nucleotide, and in addition revealed the proximity of TNP-AMP to several other residues, including Thr441, Glu442, Lys515, Arg560, and Leu562 (1).
A surprising feature of the crystal structure of the Ca2+-bound E1Ca2 dephospho form is that the configuration of the cytoplasmic domains is quite open with the nucleotide-binding site being separated from Asp351 in domain P by more than 25 Å, implying large domain movements during ATP binding and hydrolysis (1). Presumably, the binding of nucleotide leads to closing of the structure. The movements contribute to uncertainties about the nucleotide-binding residues and the orientation of the bound nucleotide. Although the high affinity binding sites for TNP-nucleotide and ATP seem to overlap (6), they are not necessarily identical. Thapsigargin, a potent inhibitor of the Ca2+-ATPase, has no effect on TNP-ATP or TNP-8N3-ATP binding, and yet decreases the affinity of the pump for ATP by at least 100-fold (5, 7). The doubts with respect to the nucleotide site are exacerbated by functional studies showing that ATP in addition to being the phosphorylating substrate exerts modulatory effects on various steps of the pump cycle, see boxed ATP in Scheme 1 (8, 9, 10, 11, 12, 13, 14, 15, 16). In view of the predicted large domain movements and presence of the phosphoryl group at the catalytic site during part of the cycle, it seems unlikely that modulatory ATP binds exactly as substrate ATP does.
In the present study, we have introduced mutations of Thr441, Glu442, Lys515, Arg560, Cys561, and Leu562, and we have also extended the previous study (5) on mutants with alterations to Phe487, Arg489, and Lys492. With the exception of Cys561, these residues show a high degree of conservation throughout the P-type ATPase family (17). A recent study, applying solution nuclear magnetic resonance techniques to a 28-kDa recombinant Ca2+-ATPase fragment corresponding to domain N pinpointed Thr441 and Glu442 as the two residues providing the largest shifts in the backbone15N spectra upon addition of a non-hydrolyzable ATP analogue to the medium (18). Marked spectral shifts were also seen for residues close in the linear sequence to Lys492, Lys515, and Arg560. Site-directed mutagenesis studies have previously shown the importance of Lys515 and Arg560 in the overall ATPase function (19, 20, 21). Mutation of Lys515 to arginine, alanine, glutamine, and glutamate resulted in 65, 30, 25, and 5% Ca2+-transport activity relative to wild type (19, 20). Mutation of Arg560 to alanine abolished phosphorylation from ATP (21). Thr441, Glu442, Cys561, and Leu562, or their homologues in other P-type ATPases, have not been subjected previously to mutational analysis.
This study, presenting the first direct measurements of nucleotide-binding properties of mutants with alterations to Thr441, Glu442, Lys515, Arg560, Cys561, and Leu562 of the Ca2+-ATPase, reveals marked effects on nucleotide binding to the substrate site of the dephosphoenzyme, except in the case of the Cys561 mutants. Moreover, our analysis of other steps in the pump cycle (Scheme 1) demonstrates that phosphorylation, the Ca2+-translocating E1PCa2
E2P conformational transition, as well as the hydrolysis of the E2P phosphoenzyme intermediate are affected to various extents by the mutations. The low affinity modulatory effects of ATP on the phosphoenzyme-processing steps are, however, not significantly affected. Finally, we provide functional evidence for close interaction between Lys515 and Glu442 in experiments demonstrating direct involvement of Glu442 in the labeling reaction of Lys515 with FITC.
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EXPERIMENTAL PROCEDURES
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Mutagenesis, Expression, and Assays of Overall FunctionOligonucleotide-directed mutagenesis of cDNA encoding the rabbit fast twitch muscle Ca2+-ATPase (SERCA1a isoform) was carried out as described previously (22). For expression, the wild-type or mutant cDNA, inserted in the pMT2 vector (23), was transfected into COS-1 cells using the calcium phosphate precipitation method (24). The microsomal fraction containing expressed wild-type or mutant Ca2+-ATPase was isolated by differential centrifugation (19). The concentration of expressed Ca2+-ATPase was quantified by a specific enzyme-linked immunosorbent assay (25) or by determination of the maximum capacity for phosphorylation by inorganic phosphate in the presence of 30% (v/v) dimethyl sulfoxide ("active site concentration," see Ref. 26). Transport of45Ca2+ into the microsomal vesicles was measured by filtration, and the ATPase activity was measured by determining the amount of Pi liberated as described previously (26).
Phosphorylation from [
-32P]ATP and32PiManual mixing experiments at various buffer and temperature conditions (detailed in the figure legends) were carried out according to the principles described previously (22, 25, 26). Transient kinetic experiments at 25 °C were performed using a Bio-Logic quench-flow module QFM-5 (Bio-Logic Science Instruments, Claix, France) as described (27). In all phosphorylation experiments, acid quenching was performed with 0.52 volumes of 25% (w/v) trichloroacetic acid containing 100 mM H3PO4. The acid-precipitated protein was washed by centrifugation and subjected to SDS-PAGE in a 7% polyacrylamide gel at pH 6.0 (28), and the radioactivity associated with the separated Ca2+-ATPase band was quantified by imaging, using a Packard CycloneTM Storage Phosphor System. Background phosphorylation levels, subtracted from all data points, were usually determined in parallel experiments with control microsomes isolated from mock-transfected COS-1 cells. In some of the dephosphorylation experiments, the constant phosphorylation level reached after the exponential decay was taken as background (usually
5% of the initial phosphorylation).
To remove contaminant ADP and AMP, the non-radioactive ATP added in millimolar concentration in dephosphorylation experiments was purified by ion exchange chromatography on a Sephadex DEAE-A25 column before use. By using an NADH-coupled spectrophotometric assay with phosphoenolpyruvate, lactate dehydrogenase, and pyruvate kinase, the purified ATP preparation was found to contain less ADP than the detection limit of 0.1 mol %.
Assays for Nucleotide BindingThe synthesis of [
-32P]TNP-8N3-ATP, the photolabeling of COS-1 cell microsomes containing wild-type or mutant Ca2+-ATPase, the inhibition by ATP, and the quantification of labeled bands by electronic autoradiography following SDS-PAGE were carried out as described previously (5, 29). Generally, the concentration of [
-32P]TNP-8N3-ATP was 3x K0.5 in the inhibition experiments with ATP (where K0.5 is ligand concentration giving half-maximum effect). Details of the buffer composition are given in the legends. CrATP-induced Ca2+ occlusion was measured as described previously (5, 30).
Calculations and Data AnalysisThe ion concentrations in the reaction buffers were calculated using the program WEBMAXC, available on the World Wide Web, and the stability constants therein (31). Generally, experiments were conducted at least twice, and the complete set of data was analyzed by nonlinear regression using the SigmaPlot program (SPSS, Inc.). Monoexponential functions were fitted to the phosphorylation and dephosphorylation time courses. The analysis of ligand concentration dependences was based on the Hill equation,
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For analysis of the [
-32P]TNP-8N3-ATP labeling data, a constant or linear component was added to represent nonspecific labeling as described (5), and the Hill coefficient was set to 1. The "true" dissociation constant for ATP and MgATP binding was calculated using the previously validated equation for competitive inhibition of the [
-32P]TNP-8N3-ATP labeling (5).
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RESULTS
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Mutagenesis and ExpressionNine Ca2+-ATPase constructs with mutations of potential nucleotide-binding residues were prepared in this study. Thr441, Glu442, and Lys515 were replaced individually with alanine. Cys561 was replaced with alanine or tryptophan; Arg560 was replaced with leucine, valine, or glutamate; and Leu562 was replaced with phenylalanine. The latter substitution was chosen to test the importance of the leucine for nucleotide binding by either introducing steric hindrance at this position or possibly enhancing the affinity for nucleotide by creating an aromatic "sandwich" for the adenine ring with Phe487. All mutants could be expressed in COS-1 cells at levels similar to that of the wild type (data not shown), allowing studies of the overall function as well as the partial reactions of the enzyme cycle. In addition, some supplementary studies of partial reactions were carried out with previously constructed mutants (5) with alterations to Phe487, Arg489, and Lys492.
Overview of Functional EffectsFig. 1A shows ATP-driven 45Ca2+ accumulation in microsomal vesicles measured in the presence of oxalate to trap Ca2+ in the lumen. The MgATP concentration was 5 mM, i.e. several hundredfold higher than required to saturate the phosphorylation reaction in wild type. All the mutants were able to transport Ca2+, albeit at reduced rates compared with wild type. The most significant reduction was seen for mutant Arg560
Glu with a Ca2+ transport rate corresponding to 17% that of the wild type, whereas
80% transport was obtained for the Cys561 mutants. The Ca2+ transport rates of the remaining six mutants were roughly half (3966%) that of wild type.

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FIG. 1. Initial overview of ATP-driven Ca2+ transport (A), ATPase activity (B), and phosphorylation from ATP (C). A, measurements of ATP-driven Ca2+ transport were performed by filtration following incubation for 5 min at 37 °C in a medium containing 20 mM MOPS/Tris (pH 6.8), 100 mM KCl, 5 mM MgATP, 5 mM potassium oxalate (included to trap Ca2+ inside the microsomal vesicles), 0.5 mM EGTA, and 0.45 mM 45CaCl2. The Ca2+ transport activity of the wild type was taken as 100%, and each mutant was related to this level following correction for the variation in expression level. B, the rate of Ca2+-activated ATP hydrolysis was determined at 37 °C in the presence (gray bars) or absence (black bars) of 1 µM Ca2+ ionophore A23187
[GenBank]
in a medium containing 50 mM TES/Tris (pH 7.0), 100 mM KCl, 7 mM MgCl2, 1 mM EGTA, 0.9 mM CaCl2 (giving a free Ca2+ concentration of 3 µM), and 5 mM ATP. Following subtraction of the background activity determined in the absence of Ca2+, the molecular activity (catalytic turnover rate) shown was calculated as the amount of Pi liberated per Ca2+-ATPase molecule/s. C, the phosphorylation with [ -32P]ATP was carried out for 5 s at 25 °C in a medium containing 40 mM MOPS/Tris (pH 7.0), 80 mM KCl, 5 mM MgCl2, 100 µM CaCl2, and either 5 µM [ -32P]ATP (gray bars) or 50 µM [ -32P]ATP (black bars). The phosphorylation level of the wild type incubated in a medium containing 100 mM MES/Tris (pH 6.0), 10 mM MgCl2, 2 mM EGTA, 30% (v/v) dimethyl sulfoxide, and 0.5 mM 32Pi for 10 min at 25 °C was taken as 100% ("active site concentration"), and all other values were related to this level following correction for the variation in expression level. Standard errors are indicated by the error bars on the columns.
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Fig. 1B shows the ATPase activity in the presence of 5 mM MgATP without oxalate, in the absence and presence of the calcium ionophore A23187
[GenBank]
. In the absence of ionophore (conditions resulting in net Ca2+ uptake in the vesicles), a similar pattern was obtained for ATP hydrolysis as for Ca2+ transport (Fig. 1B, black columns), Arg560
Glu showing the most marked reduction of turnover rate, the Cys561 mutants being wild type like, and the remaining six mutants hydrolyzing ATP at turnover rates of 4058% as compared with wild type. The good correlation between the turnover rate for ATP hydrolysis and ATP-driven accumulation of Ca2+ in the microsomes demonstrates that the coupling between ATP hydrolysis and Ca2+ transport was retained in the mutants. Addition of calcium ionophore A23187
[GenBank]
to the reaction medium increased the rate of ATP hydrolysis in the wild type 23-fold because of relief of the "back inhibition" of the rate-limiting E1PCa2
E2P transition imposed by Ca2+ accumulated at high concentrations in the microsomal vesicles. A similar increase was seen for Thr441
Ala, Glu442
Ala, Lys515
Ala, and the Cys561 mutants, whereas for Leu562
Phe and the three Arg560 mutants the ATPase activity remained essentially unaltered (Fig. 1B, gray columns). The latter result implies that a reaction step other than the E1PCa2
E2P transition is rate-limiting in the case of Leu562 Phe and Arg560 mutants.
In the Ca2+-bound E1Ca2 state, the wild-type Ca2+-ATPase forms a phosphoenzyme intermediate by reaction with MgATP (cf. Scheme 1). Fig. 1C shows the results of experiments where phosphorylation of Ca2+-saturated enzyme was carried out for 5 s at 25 °C with either 5 or 50 µM [
-32P]MgATP. For wild type, the maximum steady-state phosphoenzyme level of
80% of the total active-site concentration is close to being reached at 5 µM MgATP; also for the Cys561 mutants, there was not much difference between 5 and 50 µM MgATP. By contrast, mutants Thr441
Ala, Glu442
Ala, Lys515
Ala, and in particular Arg560
Leu, Arg560
Val, and Leu562
Phe showed much lower phosphoenzyme levels with 5 µM MgATP than with 50 µM MgATP, indicating a markedly reduced apparent affinity for the nucleotide, relative to wild type. Mutant Arg560
Glu was unable to phosphorylate significantly above the background level at either concentration of MgATP (Fig. 1C).
MgATP Dependence and Time Course of Phosphorylation from [
-32P]ATPThe MgATP concentration dependence of phosphorylation was further investigated at 0 °C, where the ATP hydrolysis rate was sufficiently low to allow the phosphorylation to be studied at submicromolar concentrations of the substrate. As seen in Fig. 2A, a 10120-fold reduction of apparent affinity for MgATP (increase of K0.5) relative to wild type was found for mutants Thr441
Ala, Glu442
Ala, Lys515
Ala, and Leu562
Phe; and for mutants Arg560
Leu and Arg560
Val, the K0.5 for MgATP was at least 3 orders of magnitude lower than that of wild type.

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FIG. 2. MgATP concentration dependence (A) and time course (B) of phosphorylation from ATP. A, wild type and mutants were phosphorylated at 0 °C for 15 s in a medium containing 40 mM MOPS/Tris (pH 7.0), 80 mM KCl, 5 mM MgCl2, 100 µM CaCl2, and varying concentrations of [ -32P]ATP as indicated. The lines show the best fits of the Hill equation with the Hill coefficient set to 1, giving the K0.5 values (in µM ± S.E.) indicated in parentheses: open circles, wild type, (0.067 ± 0.005); open squares, Thr441 Ala (6.2 ± 0.6); open triangles, Glu442 Ala (0.72 ± 0.06); reversed solid triangles, Lys515 Ala (1.6 ± 0.2); open diamonds, Arg560 Leu (>>100); solid triangles, Arg560 Val ( 100); and solid circles, Leu562 Phe (8.1 ± 1.4). The 100% value corresponds to the phosphorylation level reached at infinite ATP concentration as deduced from the fit. B, phosphorylation was carried out at 25 °C in a medium containing 40 mM MOPS/Tris (pH 7.0), 80 mM KCl, 100 µM CaCl2, 5 mM MgCl2, and 5 µM [ -32P]ATP, and the samples were acid-quenched at serial time intervals, using a Bio-Logic QFM-5 quench-flow module with mixing protocol as described previously (34). In each case, the level of phosphorylation after 5 s was taken as 100% (for a comparison of the specific phosphorylation levels of wild type and mutants after 5 s, see Fig. 1C). The lines show the best fits of a monoexponential function, giving the rate constants (in s-1 ± S.E.) indicated in parentheses: open circles, wild type (59.7 ± 2.0); open squares, Thr441 Ala (5.3 ± 0.6); open triangles, Glu442 Ala (13.3 ± 0.6); reversed solid triangles, Lys515 Ala (11.1 ± 0.8).
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Fig. 2B shows the time course of phosphorylation at 25 °C of wild type and selected mutants determined by quench-flow methodology in the presence of 5 µM [
-32P]MgATP under conditions identical to those corresponding to Fig. 1C. Leu562
Phe and the three Arg560 mutants were not included in these studies because their phosphorylation levels were too low to allow reliable pre-steady-state measurements (cf. Fig. 1C). The wild type reaches a steady-state level of phosphorylation within a few hundred milliseconds, with a slight initial over-shoot (Fig. 2B, cf. also Ref. 27). For simplicity, a monoexponential function was fitted to the data, giving an apparent rate constant kobs = 60 s-1 for the approach to steady state. In comparison, 512-fold lower kobs values were determined for mutants Thr441
Ala, Glu442
Ala, and Lys515
Ala (Fig. 2B). The kobs value decreased in the same order as the apparent MgATP affinity observed in Fig. 2A (Glu442
Ala > Lys515
Ala > Thr441
Ala).
MgATP Dependence of ATP HydrolysisFor wild-type Ca2+-ATPase, the MgATP activation profile of ATPase activity has a complex appearance, because MgATP (or ATP) in addition to being the phosphorylating substrate exerts modulatory effects on various steps of the pump cycle, cf. Scheme 1 (8, 9, 10, 11, 12, 13, 14, 15, 16). The basal activation to about 20% of the maximum activity occurring at MgATP concentrations below 10 µM in wild type reflects the binding of MgATP to the E1Ca2 form as phosphorylating substrate. It can be seen in Fig. 3 that for mutant Leu562
Phe and the three Arg560 mutants, the basal activation was shifted to much higher MgATP concentrations in agreement with the data in Fig. 2A. Less drastic right-shifts of the basal activation were observed for mutants Thr441
Ala, Glu442
Ala, and Lys515
Ala with plateau levels being reached at about 50 µM MgATP, whereas the Cys561 mutants were wild type-like. At least two secondary activation phases occur for the wild-type enzyme, between 10 and 200 µM MgATP and at higher MgATP concentrations, reflecting the accelerating effect of nucleotide on partial reaction steps preceding and subsequent to phosphorylation (9, 10, 12, 13, 14, 15, 16). Fig. 3 shows that the Cys561 mutants displayed a wild type-like secondary activation. For mutant Leu562
Phe and the three Arg560 mutants, the severely reduced ATPase activity prevented a clear distinction between the basal and the intermediate modulatory phases (Fig. 3), but a distinct low affinity activation phase similar to that of the wild type is seen above 200 µM MgATP for Arg560
Leu, Arg560
Val, and Leu562
Phe, as well as for Thr441
Ala, Glu442
Ala, and Lys515
Ala, indicating that nucleotide binding with low affinity accelerates at least one partial reaction in these mutants, although in contrast to the wild type the activation profiles level off above 3 mM MgATP for Thr441
Ala, Glu442
Ala, and Lys515
Ala. Furthermore, taking into consideration that the basal activation is shifted to higher MgATP concentrations relative to wild type, the activation occurring with intermediate affinity, between 10 and 200 µM MgATP in wild type, seems to be less pronounced or right-shifted in Thr441
Ala, Glu442
Ala, and Lys515
Ala. This is most obvious for Glu442
Ala, where the ATPase activity was nearly constant between 50 and 200 µM MgATP (Fig. 3).

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FIG. 3. MgATP dependence of ATPase activity. The rate of ATP hydrolysis was measured at 37 °C in a medium containing 50 mM TES/Tris (pH 7.5), 100 mM KCl, 100 µM CaCl2, 1 µM Ca2+ ionophore A23187
[GenBank]
, and varying concentrations of Mg2+ and ATP to give the indicated MgATP concentrations and 1 mM free Mg2+. Following subtraction of the background activity determined in the absence of Ca2+ (presence of 1 mM EGTA without CaCl2), the catalytic turnover rate shown was calculated as the amount of Pi liberated per Ca2+-ATPase molecule/s. The symbols are as follows: open circles, wild type; reversed open triangles, Cys561 Ala; solid squares, Cys561 Trp; solid triangles, Arg560 Val; open diamonds, Arg560 Leu; solid diamonds, Arg560 Glu; open squares, Thr441 Ala; open triangles, Glu442 Ala; reversed solid triangles, Lys515 Ala and solid circles, Leu562 Phe.
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Acetyl Phosphate-driven Ca2+ UptakeAs an alternative to ATP, acetyl phosphate can be used as an energy source to drive Ca2+ transport into the microsomal vesicles (16). Fig. 4 shows the time course for wild type and the mutants. For most mutants, the decrease of the transport rate relative to wild type was rather similar to the decrease seen for ATP-driven transport at 5 mM MgATP (Fig. 1A), as also shown previously for mutant Lys515
Ala (20), indicating that at high MgATP concentration (Fig. 1, A and B) the limitation of the overall reaction rate seen for the mutants is not imposed by binding defects specific to the nucleotide, but rather by defects in other partial reaction steps. Interestingly, mutant Leu562
Phe is a clear exception to this pattern. This mutant showed a markedly reduced ATP-driven Ca2+ transport (Fig. 1A) and ATPase activity (Fig. 1B), but wild type-like acetyl phosphate-dependent Ca2+ transport (Fig. 4).

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FIG. 4. Acetyl phosphate-driven Ca2+ transport. Transport activity of COS-1 cell microsomes was measured at 25 °C in 25 mM MOPS/Tris (pH 6.8), 100 mM KCl, 5 mM MgCl2, 0.55 mM 45CaCl2, 0.5 mM EGTA, 5 mM potassium oxalate, and 10 mM acetyl phosphate for the times shown. The ordinate shows the amount of Ca2+ accumulated per mg of Ca2+-ATPase protein. The symbols are as follows: open circles, wild type; open squares Thr441 Ala; open triangles, Glu442 Ala; reversed solid triangles, Lys515 Ala; solid triangles, Arg560 Val; open diamonds, Arg560 Leu; solid diamonds, Arg560 Glu; reversed open triangles, Cys561 Ala; and solid circles, Leu562 Phe.
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Ca2+ DependenceTo examine whether a reduced affinity for Ca2+ could be involved in the observed effects of the mutations on Ca2+ transport and ATPase activity, we performed a Ca2+ titration of the ATPase activity. The Ca2+ concentration giving half-maximum activation of ATP hydrolysis was 0.33 ± 0.01 µM for the wild type and 0.64 ± 0.05, 0.41 ± 0.02, 0.35 ± 0.02, 0.33 ± 0.02, 0.54 ± 0.04, 0.38 ± 0.02, 0.47 ± 0.04, and 0.38 ± 0.03 µM for Arg560
Leu, Arg560
Val, Cys561
Ala, Cys561
Trp, Leu562
Phe, Thr441
Ala, Glu442
Ala, and Lys515
Ala, respectively (the K0.5 value was obtained by fitting the Hill equation, ± S.E., from the regression analysis, data not shown). Thus, although significant alterations to Ca2+ binding are evident for mutants Arg560
Leu and Leu562
Phe, the mutants were >80% saturated with Ca2+ at the free Ca2+ concentration of 3 µM present during the experiments corresponding to Fig. 1, A and B, and close to 100% saturated at the higher free Ca2+ concentrations present during the experiments corresponding to Fig. 1C, Fig. 2, A and B, Fig. 3, and Fig. 4. Hence, the observed effects of the mutations cannot be ascribed to variable Ca2+ saturation.
Nucleotide BindingTo examine the mutational effects on nucleotide binding directly, we applied a photolabeling assay that takes advantage of the highly specific labeling of Lys492 with [
-32P]TNP-8N3-ATP (5). In this assay, the affinities for the free and Mg2+-bound forms of [
-32P]TNP-8N3-ATP are determined from the dependence of photolabeling on the concentration of the label in the absence and presence of Mg2+, respectively. By studying competitive inhibition of photolabeling in the presence of varying concentrations of ATP and MgATP (the latter often being referred to as the "true" substrate (32)), it is also possible to obtain highly accurate values for the KD corresponding to these nucleotides (5, 33, 34). Photolabeling is carried out in the absence of Ca2+ to avoid phosphorylation of the Ca2+-ATPase and hydrolysis of the photolabel, and at pH 8.5 to reduce nonspecific labeling and ensure that the predominant enzyme conformation is E1 (5). Results of photolabeling experiments with the nine mutants in the absence and presence of Mg2+ are summarized in Table I. Also presented here for the first time are nucleotide-binding parameters in the absence of Mg2+ for mutants Phe487
Leu, Arg489
Leu, and Lys492
Tyr of the487FSRDRK loop in domain N. These latter mutants have only been analyzed previously in the presence of Mg2+ (5). We have shown before (33, 34), and reproduced in Table I, that wild type exhibits a striking Mg2+ dependence for both TNP-8N3-ATP and ATP binding; Mg2+ lowers the apparent affinity for the TNP-nucleotide and increases (as much as 40-fold) that for ATP.
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TABLE I Nucleotide binding parameters in the presence and absence of Mg2+
Photolabeling with [ -32P]TNP-8N3-ATP was carried out as described in Ref. 5 and competition with ATP/MgATP as described in Ref. 5 and illustrated in Fig. 5. The parameters shown were derived from analysis of the data as described for Fig. 5 and under "Experimental Procedures."
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The two Cys561 mutants differed little from wild type in the binding assays, whereas the remaining mutants showed interesting differences from wild type (Table I). Examining the interaction with TNP-8N3-ATP and TNP-8N3-MgATP first, there were major changes relative to wild type in both labeling efficiency and in the apparent affinity for the photolabel. Lys515
Ala and Arg560
Glu showed no specific photolabeling above the background level either in the absence or presence of Mg2+, and Arg560
Val could not be labeled in the absence of Mg2+. Arg560
Leu and Arg560
Val showed conspicuous
10-fold decreases, relative to wild type, of the apparent affinity for the photolabel (i.e. increased K0.5) in the presence of Mg2, whereas Thr441
Ala, Glu442
Ala, and Leu562
Phe showed slight increases of the apparent affinity (i.e. reduced K0.5). It is evident that Arg560 plays a major role in binding the TNP-nucleotide in the presence of Mg2+. On the other hand, Arg560
Leu showed no significant deviation from wild type in the absence of Mg2+. In Thr441
Ala, the ability to respond to Mg2+ with a reduced affinity for the TNP-nucleotide was lost; in the presence of Mg2+ this mutant displayed an affinity for the photolabel similar to or slightly higher than that displayed in the absence of Mg2+, whereas in the wild type Mg2+ reduces the affinity for the photolabel. With respect to the three mutants with alterations to residues of the 487FSRDRK loop, Arg489
Leu and Lys492
Tyr showed a large decrease in affinity for the photolabel relative to wild type in the absence of Mg2+, corresponding to 31- and 17-fold, respectively, whereas Phe487
Leu exhibited an increased affinity. Evidently the two basic amino acid residues are critical for binding the nucleotide in the absence of Mg2+.
Although the binding sites for ATP and TNP-8N3-ATP may not be identical, there is sufficient overlap to ensure efficient competition when ATP or MgATP is added at varying concentrations during photolabeling, and we have previously demonstrated that the competition assay provides highly accurate values for the ATP and MgATP binding affinities of wild type and mutant Ca2+-ATPases expressed in COS-1 cells (5). For wild type, the true affinities (KD values) for MgATP and ATP calculated under the assumption of competitive inhibition as described previously (5) were found to be 0.51 and 21 µM, respectively (Table I). Fig. 5 shows examples of the experimental data from which the KD values for ATP and MgATP in Table I were derived, corresponding to Thr441
Ala, Glu442
Ala, Arg560
Leu, and Leu562
Phe, with data for wild type (see also Refs. 5 and 33) indicated by dashed lines without data points. Because of the deficient photolabeling described above, competition experiments could not be carried out for Lys515
Ala and Arg560
Glu. Mutation Arg560
Leu decreased the affinity (i.e. increased KD) for MgATP more than 1000-fold, whereas mutations Cys561
Ala and Cys561
Trp had little effect, as mentioned above. A decrease of affinity for MgATP of 40-fold relative to wild type was seen for Arg560
Val, and as much as 70180-fold for Thr441
Ala, Glu442
Ala, and Leu562
Phe. In the absence of Mg2+, Arg560
Leu still showed a conspicuous 30-fold decrease of affinity for ATP, whereas for Thr441
Ala, Glu442
Ala, and Leu562
Phe, the affinity for ATP was only 25-fold reduced relative to wild type.
In the case of the487FSRDRK mutants, Arg489
Leu and Lys492
Tyr showed extremely poor binding of ATP in the absence of Mg2+, reproducing what was found for the TNP-nucleotide. For Phe487
Leu the changes in the presence and absence of Mg2+ were rather similar, 1020-fold reduced affinity compared with wild type.
For Thr441
Ala and Arg560
Leu, competition studies were also carried out with ADP. For wild type, the KD values for ADP in the presence and absence of Mg2+ were 4 and 28 µM, respectively. For both Thr441
Ala and Arg560
Leu, there were pronounced decreases in affinity for ADP as well as MgADP (8- and >100-fold, respectively, for ADP, and
30- and
200-fold, respectively, for MgADP).
CrATP-induced Ca2+ OcclusionThe conspicuous effects found in the above-described experiments testing the nucleotide-binding properties of the mutants, and the uncertainty with respect to Lys515
Ala, because it could not be photolabeled with TNP-8N3-ATP, encouraged us to study, as an alternative, the binding of another nucleotide, the non-phosphorylating
,
-bidentate chromium(III) complex of ATP ("CrATP"). In the wild type, CrATP binds with relatively low affinity, forming a very stable complex with the enzyme, in which Ca2+ is "occluded" at the transmembranous high affinity Ca2+ sites (30, 35). The high stability of the Ca2+-occluded CrATP-enzyme complex upon removal of free CrATP from the medium (35) makes it feasible to quantify the complex by size-exclusion chromatography of detergent-solubilized microsomal protein following incubation with CrATP in the presence of radioactive 45Ca2+, and we have previously demonstrated a correlation between deficient CrATP-induced 45Ca2+ occlusion and defective ATP binding in mutants of the Ca2+-ATPase (5, 33). Because the Ca2+ titration of ATPase activity described above indicated that all the mutant enzymes bind Ca2+ with an affinity similar or close to that of wild type, the Ca2+ sites are saturated at the 45Ca2+ concentration of 40 µM used here, and the amount of 45Ca2+ occluded should, therefore, reflect the ability to bind CrATP. Fig. 6 shows 45Ca2+ elution profiles obtained for wild type and selected mutants, as well as for control microsomes harvested from cells transfected with the expression vector without insert. For wild type, a distinct peak is seen at 1415 min of retention time, corresponding to the elution of Ca2+-ATPase, whereas the control only shows a rather broad peak extending between 10 and 16 min of retention time. The difference between the test and control curves at 1415 min of retention time provides a measure of 45Ca2+ bound in the occluded state in the Ca2+-ATPase. For mutant Thr441
Ala, a minor peak of radioactivity was evident at the position corresponding to Ca2+-ATPase, indicating partial, but extremely reduced, formation of the Ca2+-occluded CrATP-enzyme complex in the present incubation conditions. No such peak was obtained in experiments performed with mutants Glu442
Ala, Lys515
Ala, Arg560
Leu, and Leu562
Phe (Fig. 6), or with Arg560
Val and Arg560
Glu (data not shown). For the Cys561 mutants, the 45Ca2+ peak corresponding to Ca2+-ATPase was similar to that seen for wild type (data not shown). Thus, the effects of the mutations on formation of the Ca2+-occluded CrATP-enzyme complex are in accordance with the effects on MgATP binding described above, and Lys515
Ala is clearly included among the mutants showing defective nucleotide binding.

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FIG. 6. CrATP-dependent Ca2+ occlusion. Wild-type or mutant Ca2+-ATPase expressed in COS-1 cell microsomes was incubated for 1 h at 37 °C in 50 mM TES/Tris (pH 7.0), 100 mM NaCl, 5 mM MgCl2, 40 µM 45CaCl2, and 1 mM CrATP. At the end of the incubation period, the membranes were solubilized by addition of 5 mg/ml of the non-ionic detergent C12E8. Following centrifugation, the supernatant was subjected to size-exclusion high pressure liquid chromatography as described previously (5). The elution buffer contained 50 mM TES/Tris (pH 7.0), 100 mM NaCl, 10 mM MgCl2, 1.5 mM CaCl2, 1 mM EGTA, and 2 mg/ml C12E8. The solid circles show the radioactivity in collected fractions. The result of a control experiment with microsomes harvested from cells transfected with the expression vector without insert is indicated by the thin line without data points. The difference between the test and control curves at 1415 min of retention time, corresponding to the elution of Ca2+-ATPase, provides a measure of the occluded 45Ca2+. The amount of mutant Ca2+-ATPase protein applied to the column was roughly equivalent to the amount of wild type (±30%, due to variation of the expression level, as determined by enzyme-linked immunosorbent assay).
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The E1PCa2 to E2P Conformational TransitionTo examine the effects of the mutations on the E1PCa2
E2P transition, we determined the rate of decay of phosphoenzyme under conditions (0 °C, presence of K+, and neutral pH) where the E1PCa2
E2P transition is rather slow and, thus, rate-limiting for the dephosphorylation, whereas the subsequent hydrolysis of E2P (Scheme 1) is relatively rapid. The phosphorylation by [
-32P]MgATP was terminated by addition of an excess of EGTA (to remove Ca2+). As seen in Fig. 7 and Table II (column marked "EGTA," i.e. no addition of non-labeled MgATP), the rate of phosphoenzyme decay was reduced as much as 68-fold relative to wild type, for mutants Thr441
Ala, Glu442
Ala, and Lys515
Ala. Leu562
Phe deviated much less from wild type. Among the Arg560 mutants, only Arg560
Val could be examined, because of the very low phosphorylation levels obtained with the other two Arg560 mutants at 0 °C. It appears from Fig. 7 and Table II that Arg560
Val showed a unique 2-fold enhancement of the rate of phosphoenzyme decay, relative to wild type.

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FIG. 7. Dephosphorylation at 0 °C of phosphoenzyme formed from ATP. Phosphorylation was performed for 15 s at 0 °C in a medium containing 40 mM MOPS/Tris (pH 7.0), 80 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.955 mM CaCl2 (giving a free Ca2+ concentration during phosphorylation of 10 µM), 10 µM calcium ionophore A23187
[GenBank]
, and 5 µM [ -32P]ATP (50 µM in case of Arg560 Val, because of its low affinity, cf. Fig. 2A). To measure dephosphorylation, the phosphoenzyme was chased by addition of 10 mM EGTA (solid triangles), 10 mM EGTA with 1 mM non-radioactive MgATP (open circles), or 10 mM EGTA with 5 mM non-radioactive MgATP (solid circles), and acid quenching was performed at the indicated time intervals. The lines show the best fits of a monoexponential decay function; the rate constants are listed in Table II.
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FIG. 9. Dephosphorylation of phosphoenzyme formed from Pi. Wild type and mutants were phosphorylated at 25 °C for 10 min in a medium containing 100 mM MES/Tris (pH 6.0), 2 mM EGTA, 30% (v/v) dimethyl sulfoxide, 10 mM MgCl2, and 0.5 mM 32Pi. Dephosphorylation was studied at 25 °C by a 19-fold dilution into a medium containing EDTA (to remove free Mg2+) corresponding to a final concentration of 10 mM, 100 mM MES/Tris (pH 6.0), 2 mM EGTA, 15% (v/v) dimethyl sulfoxide, 0.5 mM non-radioactive Pi, without (open circles) or with (solid circles) 1 mM ATP, followed by acid quenching at serial time intervals. The lines show the best fits of a monoexponential decay function; the rate constants are listed in Table II.
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To test the low affinity modulatory effect of the nucleotide on the E1PCa2
E2P transition (cf. Scheme 1, boxed ATP), the dephosphorylation was also examined at 1 and 5 mM non-labeled MgATP added with EGTA. It can be seen in Fig. 7 and Table II that the nucleotide induced a significant enhancement of the dephosphorylation rate in the wild type as well as the mutants. Both in wild type and in Thr441
Ala, Glu442
Ala, Lys515
Ala, Arg560
Val, and Leu562
Phe the rate constant observed at 5 mM MgATP was roughly 2-fold higher than that observed at 1 mM MgATP, which is surprisingly consistent with the increase of ATPase activity in this concentration range (Fig. 3), taking into account the different temperatures under which these experiments were carried out.
Table II also shows the results of similar measurements performed with mutants Phe487
Leu, Arg489
Leu, and Lys492
Leu, whose MgATP and ATP affinities at the substrate site were reported in the previous paper (5) and in Table I of the present paper, respectively. Lys492
Leu showed a conspicuous 6-fold slowing of the phosphoenzyme decay observed upon EGTA addition, whereas only small differences from wild type were seen for Phe487
Leu and Arg489
Leu. For all 3 mutants, there was a substantial modulatory effect of millimolar MgATP, although slightly less pronounced than for the wild type and the above-described mutants (1.41.6-fold enhancement from 1 to 5 mM MgATP).
ADP Sensitivity of the PhosphoenzymeThe two phosphoenzyme intermediates E1PCa2 and E2P can normally be distinguished by their different sensitivity to ADP. E1PCa2 is ADP-sensitive, i.e. able to donate the phosphoryl group back to ADP, forming ATP, whereas E2P is insensitive to ADP and dephosphorylates only by hydrolysis. To test the ADP sensitivity, 1 mM ADP was added following phosphorylation under the same conditions as described for Fig. 7. This resulted in almost complete dephosphorylation of wild type within 5 s, demonstrating accumulation of the E1PCa2 form of the phosphoenzyme, and similar effects of ADP were seen for all the mutants studied except Arg560
Val, for which as much as 24% phosphoenzyme remained after the 5-s incubation with ADP (Table II), indicating a significantly reduced sensitivity to ADP. This could be the result of accumulation of E2P, as a consequence of the enhancement of the E1PCa2
E2P transition reported above. Alternatively, the reduced ADP sensitivity reflects a lowered affinity of the E1PCa2 form for ADP. This would be in keeping with the very pronounced decrease in affinity for MgADP and ADP shown above for Arg560
Leu (Table I).
Properties of the E2P PhosphoenzymeThe E2P phosphoenzyme can be formed by "backward" phosphorylation with inorganic phosphate of the E2 state in the absence of Ca2+ and presence of Mg2+ (cf. Scheme 1). Fig. 8 shows the phosphorylation at varying concentrations of 32Pi under conditions optimal for stabilization of the E2P phosphoenzyme (acidic pH, presence of the organic solvent dimethyl sulfoxide, and absence of alkali metal ions). The concentration of Pi giving half-maximum phosphorylation is close to 10 µM for wild type. Significantly reduced apparent affinity (increased K0.5) for Pi was seen for Glu442
Ala and Lys515
Ala (5- and 2.5-fold, respectively), whereas Arg560
Leu and Arg560
Val showed 2-fold increased apparent affinity for Pi. Minor shifts were also seen for mutants Thr441
Ala and Cys561
Ala (K0.5 1.5-fold increased and 1.5-fold decreased, respectively), whereas mutants Arg560
Glu and Leu562
Phe (Fig. 8), as well as Cys561
Trp (not shown), were indistinguishable from wild type. It is important to stress here that because the K0.5 is a function of several kinetic constants, it should not necessarily correlate with the true dissociation constant, KD, describing the non-covalent enzyme-Pi complex (E2·Pi in Scheme 1). As discussed previously (34), the respective rate constants, k2 and k-2, for formation and hydrolysis of the covalent bond in E2P may be important as well. To study k-2, the wild type and selected mutants were phosphorylated under optimal conditions for formation of the E2P phosphoenzyme, followed by dilution at 25 °C into a medium of the same composition except for the absence of radioactively labeled Pi, a reduction of the dimethyl sulfoxide concentration from 30 to 15%, and the presence of excess EDTA to remove free Mg2+ and thus terminate phosphorylation (Fig. 9 and Table II). It should be noted that because of the acidic pH, absence of K+, and presence of 15% dimethyl sulfoxide, the rate of dephosphorylation of E2P is much slower than under physiological conditions. For mutants Glu442
Ala and Lys515
Ala, the reduced apparent affinities for Pi (Fig. 8) were well accounted for by significantly increased rates of E2P hydrolysis (5- and 3.5-fold, respectively). A similar increase was noted for Lys492
Leu (Table II). For mutant Thr441
Ala, a slightly (1.4-fold) increased rate of E2P hydrolysis (Fig. 9) explains the 1.5-fold increased K0.5 (Fig. 8). Leu562
Phe, Phe487
Ser, Phe487
Leu, and Arg489
Leu also showed slight increases of the rate of E2P hydrolysis, and the Cys561 mutants (data not shown) were indistinguishable from wild type. Interestingly, mutant Arg560
Glu showed a conspicuous 5-fold increase of the rate of E2P hydrolysis (Fig. 9), despite its wild type-like apparent affinity for Pi (Fig. 8). In analogy with this discrepancy, mutants Arg560
Leu and Arg560
Val showed wild type-like rates of E2P hydrolysis (Fig. 9), but 2-fold increased apparent affinities for Pi (Fig. 8). Thus, for the Arg560 mutants, an increase of the true affinity for Pi (KD) or an increased rate constant for formation of the covalent bond in E2P (k2) must contribute to the change (and lack thereof) in the apparent affinity for Pi.

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FIG. 8. Phosphorylation from Pi. Wild type and mutants were phosphorylated at 25 °C for 10 min in a medium containing 100 mM MES/Tris (pH 6.0), 2 mM EGTA, 30% (v/v) dimethyl sulfoxide, 10 mM MgCl2, and varying concentrations of 32Pi as indicated. The lines show the best fits of the Hill equation with the Hill coefficient set to 1, giving the K0.5 values (in µM ± S.E.) indicated in parentheses: open circles, wild type (10.5 ± 0.6); open squares, Thr441 Ala (16.4 ± 1.5); open triangles, Glu442 Ala (52.8 ± 8.2); reversed solid triangles, Lys515 Ala (27.5 ± 5.2); open diamonds, Arg560 Leu (4.8 ± 0.4); solid triangles, Arg560 Val (5.0 ± 0.4); solid diamonds, Arg560 Glu (9.0 ± 1.0); reversed open triangles, Cys561 Ala (6.9 ± 0.4); and solid circles, Leu562 Phe (10.6 ± 0.9). The 100% value corresponds to the phosphorylation level reached at infinite Pi concentration as deduced from the fit.
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Fig. 9 and Table II furthermore show that inclusion of 1 mM ATP enhanced the dephosphorylation of E2P close to 2-fold in the wild type and all the mutants studied, thus indicating that the modulatory effect of ATP on this partial reaction step (cf. boxed ATP in Scheme 1) is as unaffected by the mutations as the low affinity modulatory effect on the E1PCa2
E2P transition described above. Because the modulation of E2P
E2 has been ascribed to metal-free ATP rather than the MgATP complex (14), it is important to note here that when ATP was included in the assay for dephosphorylation of E2P, the ATP was present in the metal-free form as a consequence of the co-addition of excess EDTA, unlike the assay for the E1PCa2
E2P transition described above, where the major fraction of the ATP was present as MgATP.
Reaction of Lys515 with FITCFITC is a potent inhibitor of Ca2+-ATPase activity (2) and acts by specific covalent attachment to Lys515 (3), blocking high affinity ATP binding (2). The specificity of the reaction is mainly due to a high affinity of FITC for the nucleotide site rather than an unusual high reactivity of Lys