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Protein Science (2003), 12:532-537.
Copyright © 2003 The Protein Society

Asparagine 285 plays a key role in transition state stabilization in rabbit muscle creatine kinase

Charles L. Borders, Jr., Katherine M. MacGregor, Paul L. Edmiston, Elikem R.K. Gbeddy, Michael J. Thomenius, Guy B. Mulligan and Mark J. Snider

Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, USA

Reprint requests to: Charles L. Borders, Jr., Department of Chemistry, College of Wooster, Wooster, OH 44691, USA; e-mail: borders{at}wooster.edu; fax: (330) 263-2386.

(RECEIVED August 27, 2002; FINAL REVISION November 26, 2002; ACCEPTED November 26, 2002)

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.0230403.

1 All CK residues are numbered using the sequence of rabbit muscle CK reported elsewhere (Chen et al. 1996; Edmiston et al. 2001). Back

2 Rabbit muscle creatine kinase follows a random-order, rapid-equilibrium mechanism in the direction of phosphocreatine synthesis (Morrison and James 1965). Since the formation of the catalytically competent EAC complex (see Fig. 3Go) arises from two successive binding steps described by Kd(A)*KM(C) ( = Kd(C)*KM(A)), the catalytic efficiency is defined as kcat/Kd(C)*KM(A). Back


    Abstract
 TOP
 Abstract
 Introduction
 Results
 Discussion
 Conclusion
 Materials and methods
 References
 
To explore the possibility that asparagine 285 plays a key role in transition state stabilization in phosphagen kinase catalysis, the N285Q, N285D, and N285A site-directed mutants of recombinant rabbit muscle creatine kinase (rmCK) were prepared and characterized. Kinetic analysis of phosphocreatine formation showed that the catalytic efficiency of each N285 mutant was reduced by approximately four orders of magnitude, with the major cause of activity loss being a reduction in kcat in comparison to the recombinant native CK. The data for N285Q still fit a random-order, rapid-equilibrium mechanism, with either MgATP or creatine binding first with affinities very nearly equal to those for native CK. However, the affinity for the binding of the second substrate is reduced approximately 10-fold, suggesting that addition of a single methylene group at position 285 disrupts the symphony of substrate binding. The data for the N285A mutant only fit an ordered binding mechanism, with MgATP binding first. Isosteric replacement to form the N285D mutant has almost no effect on the KM values for either creatine or MgATP, thus the decrease in activity is due almost entirely to a 5000-fold reduction in kcat. Using the quenching of the intrinsic CK tryptophan fluorescence by added MgADP (Borders et al. 2002), it was found that, unlike native CK, none of the mutants have the ability to form a quaternary TSAC. We use these data to propose that asparagine 285 indeed plays a key role in transition state stabilization in the reaction catalyzed by creatine kinase and other phosphagen kinases.

Keywords: Creatine kinase; asparagine 285; mutagenesis; transition state stabilization

Abbreviations: CK, creatine kinase • AK, arginine kinase • TSAC, transition-state analog complex


    Introduction
 TOP
 Abstract
 Introduction
 Results
 Discussion
 Conclusion
 Materials and methods
 References
 
Creatine kinase1 (CK; EC 2.7.3.2) is a key enzyme in excitable tissues which require large energy fluxes, such as skeletal muscle, heart muscle, and brain (Watts 1973; Kenyon and Reed 1983; Wallimann et al. 1992). It catalyzes the readily reversible phosphorylation of creatine by MgATP to form phosphocreatine and MgADP. The forward reaction is favored by higher pH, whereas the reverse reaction is favored by an increase in acidity. In tissue such as skeletal muscle, rapid metabolic activity leads to increased acidity, and thus the production of ATP, whereas the resting state of muscle favors the formation of phosphocreatine. CK can thus be thought of as an ATP buffer in excitable tissue.

CK is a member of a larger family of phosphagen kinases that catalyze the reversible phosphorylation of a guanidino substrate by MgATP. CK is the only phosphagen kinase found in vertebrates (Watts 1973). In lower life forms, the role of CK is usually filled by other phosphagen kinases that use different guanidino substrates. Arginine kinase (AK) is most common in these instances (Morrison 1973), but other phosphagen kinases have also been reported. AK, found in insects and crustaceans as well as other lower life forms, has a high sequence homology with CK (Mühlebach et al. 1994; Suzuki and Furukohri 1994; Edmiston et al. 2001), suggesting that both enzymes apparently evolved from a common ancestral protein over evolutionary time (Morrison 1973; Watts 1973; Mühlebach et al. 1994; Suzuki and Furukohri 1994; Edmiston et al. 2001).

There are numerous recent reports on x-ray crystal structures of various creatine kinases, including the chicken mitochondrial (Fritz-Wolf et al. 1996), rabbit muscle (Rao et al. 1998), chicken brain (Eder et al. 1999), human mitochondrial (Eder et al. 2000), bovine brain (Tisi et al. 2001), and human muscle (Shen et al. 2001) enzymes. However, none of these structures contain functionally bound substrates or inhibitors that might give some insight into residues involved in binding and catalysis. The 1.8 Å crystal structure of AK (Zhou et al. 1998) contains the arginine•nitrate•MgADP transition-state analog complex (TSAC) and is very useful in identifying key active-site residues in phosphagen kinases. The planar nitrate in the AK TSAC (Fig. 1Go), which lies on a line between a terminal oxygen from the ß-phosphate of ADP and a terminal guanidino nitrogen from the substrate arginine, mimics the planar {gamma}-phosphate in the transition state for transfer between these two atoms. The nitrate interacts with the Mg(II), and also forms two hydrogen bonds with Arg3192, a third with Arg235, a fourth with Asn285, and a fifth with a water molecule (Fig. 2Go). Asn285 also makes a hydrogen bond to the same water, as well as to Arg340, which also makes a hydrogen bond to the same water. We have kinetic evidence that suggests that mutagenesis of either Arg235 or Arg319 to a lysine residue causes a significant loss of activity (C.L. Borders, Jr., and P.R. Geiss, unpubl.), and thus these residues may be critical for transition-state stabilization. We now report, based on the properties of the N285Q, N285A, and N285D mutants, that Asp285 also plays a key role in transition-state stabilization in CK, as well as a possible role in the determination of the mechanism of catalysis.



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Figure 1. Stereoview of the MgADP•nitrate•arginine transition-state analog complex (TSAC) bound to the active site of horseshoe crab AK (Zhou et al. 1998). The Mg(II) is ligated by oxygen atoms from the nitrate and the {alpha}- and ß-phosphates, and the planar nitrate is perpendicular to a direct line (gray) from an oxygen on the ß-phosphate to a terminal guanidino nitrogen of the substrate arginine, with its N atom lying on the line and approximately halfway in between. Prepared from PDB #1bg0 using Kinemage.

 


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Figure 3. The random-order, rapid-equilibrium mechanism for the forward reaction catalyzed by CK. Either MgATP (A) or creatine (C) may bind first to form a binary complex (EA or EC), to which the second substrate binds to form the catalytically competent ternary complex (EAC).

 


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Figure 2. Stereoview of horseshoe crab AK (Zhou et al. 1998) showing the multiple interactions of the nitrate moiety of the MgADP-nitrate•arginine TSAC with amino acid residues at the active site. All residues shown are fully conserved in all phosphagen kinases and are numbered using the numbering system for rabbit muscle CK (Chen et al. 1996; Edmiston et al. 2001). Noncovalent interactions are shown in gray. Prepared from PDB #1bg0 using Kinemage.

 

    Results
 TOP
 Abstract
 Introduction
 Results
 Discussion
 Conclusion
 Materials and methods
 References
 
Kinase activity
A kinetic analysis of the forward reaction (phosphocreatine formation) of the N285Q, N285A, and N285D mutants of creatine kinase was carried out at pH 9.00 and 30°C. The results (Table 1Go) indicate that the catalytic efficiency3 of each mutant was significantly reduced by approximately four orders of magnitude, with the major cause of activity loss being a 1200–5000-fold reduction in kcat in comparison to the recombinant native enzyme. The N285Q mutant appears to follow the same random-order mechanism as the native CK; however, the binding of the second substrate is characterized by a higher KM. In contrast, the data for the N285A mutant only fit an ordered binding mechanism, with MgATP binding first. The activity of the N285D mutant was very low, limiting full kinetic analysis, but KM values for both MgADP and creatine are very similar to those obtained for the native enzyme, suggesting that the loss of activity is due almost entirely to a reduction in kcat.


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Table 1. Kinetic analyses of the N285Q, N285A, and N285D mutants of rabbit muscle creatine kinasea
 
ATPase activity
CK has been reported to have a low residual ATPase activity (Sasa and Noda 1964). The specific ATPase activity (µmole/min/mg) of recombinant native CK and its N285Q, N285A, and N285D mutants was determined using 1.0 mM MgATP at pH 9.00 and 30.0°C. Table 2Go shows the data obtained, as well as the specific kinase activity of each enzyme. The native enzyme displayed a specific activity of 6.7 x 10-5 µmole/min/mg, and each mutant had a significantly lower ATPase activity than the native enzyme.


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Table 2. ATPase- and kinase-specific activities of recombinant native rabbit muscle creatine kinase and its N285Q, N285A, and N285D mutants
 
Apparent Kd for MgADP under various conditions
We recently used the quenching of the intrinsic CK tryptophan fluorescence by added nucleotide to show that the simultaneous presence of creatine and nitrate lowers the apparent Kd for MgADP by an order of magnitude (Table 3Go), strongly suggesting the formation of a quaternary creatine•nitrate•MgADP•CK TSAC (Borders, Jr. et al. 2002). We used fluorescence quenching of each N285 mutant by added MgADP in 50 mM bicine, 5 mM MgOAc, pH 8.30, 30°C to determine the Kd for this nucleotide under four sets of conditions: (1) no added creatine or nitrate, (2) 80 mM creatine but no nitrate, (3) 10 mM nitrate but no creatine, and (4) 80 mM creatine, 10 mM nitrate. The recombinant native CK shows the same apparent Kd of approximately 140 µM under the first three sets of conditions, but the value is lowered to 14 µµ when creatine and nitrate are present (Table 3Go; Borders, Jr. et al. 2002). All three N285 mutants still bind MgADP with high affinity, with the N285Q and N285D mutants displaying even lower apparent Kd values than the native CK (Table 3Go). However, two noticeable differences between the mutants and the native enzyme are apparent. First, the apparent Kd values for the mutants are not significantly lowered by the simultaneous presence of creatine and nitrate, and the second difference is that {Delta}%F on saturation of each of the mutants with MgADP is significantly greater than the corresponding value for native CK under most conditions. The only exception is when both creatine and nitrate are present during titration; this will be discussed below.


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Table 3. Effects of creatine and nitrate on the fluorescence quenching titration of creatine kinase with MgADP
 

    Discussion
 TOP
 Abstract
 Introduction
 Results
 Discussion
 Conclusion
 Materials and methods
 References
 
Catalysis by rabbit muscle CK follows a random-order, rapid-equilibrium mechanism (Fig. 3Go; Morrison and James 1965) involving in-line transfer of the {gamma}-phosphate (Hansen and Knowles 1981). Kinetic analysis of recombinant native CK shows no evidence of synergism of substrate binding (Edmiston et al. 2001), which is contrary to earlier reports that the native enzyme isolated from rabbit muscle displays synergism (Morrison and James 1965; Maggio et al. 1977). Each of the N285 mutants examined in the present study displays a greatly reduced kcat (Table 1Go), and in addition shows other interesting altered kinetic properties. The data for the N285Q mutant still fit a random-order, rapid-equilibrium mechanism, with kcat approximately 1200-fold lower than that of the native enzyme, with the apparent Kd for the binding of either MgATP or creatine first to form the binary EA or EC complex remaining essentially unchanged in comparison to the native enzyme. However, the affinity of the N285Q mutant for the second substrate to form the catalytically competent ternary complex is reduced approximately 10-fold. The extra methylene moiety introduced by isofunctional replacement of asparagine 285 by glutamine is apparently sufficient to disrupt the symphony of substrate binding.

Isosteric replacement of the asparagine 285 side chain by aspartate to form the N285D mutant has almost no effect on the KM values for creatine and MgATP, relative to the recombinant native CK, and thus its decrease in catalytic efficiency is due almost exclusively to a 5000-fold decrease in kcat (Table 1Go). These results strongly suggest that N285 plays an important role in transition-state stabilization by the native enzyme.

Attempts to fit the kinetic data for the N285A mutant to a random-order, rapid-equilibrium mechanism gave errors for the Kd values that were greater than the values of Kd itself. The only fit that gave reasonable results was to an ordered binding mechanism, with MgATP binding first (Table 1Go). Although more work is necessary to prove the possibility, it appears likely that removing the asparagine side chain and replacing it with a methyl group makes catalysis by the "normal" random-order, rapid-equilibrium mechanism impossible. The N285A mutant appears to utilize an alternative kinetic mechanism to achieve the minimal catalytic rate enhancement observed. These results again support a strong role for N285 in transition-state stabilization in native CK.

Sasa and Noda (1964) reported almost 40 years ago that CK has a very low ATPase activity, amounting to 0.0013% that of the kinase activity. Numerous investigators over the years have proposed that one catalytic role of CK is to exclude water during catalysis and thus prevent ATP hydrolysis. Structural studies (Zhou et al. 2000) indicate that AK undergoes large conformational changes when it binds the TSAC. These changes include a hinged 13° rotation of the large and small subunits towards one another and the fixation of several loops to shield the active site on TSAC binding. Those authors suggest that one major reason for the conformational compaction may be to exclude water from the active site to avoid ATP hydrolysis (Zhou et al. 2000). It is thus interesting to note that the site-bound nitrate in the AK TSAC (Zhou et al. 1998), which mimics the planar {gamma}-phosphate during catalysis (Fig. 1Go), forms a hydrogen bond to a water molecule, and that this same water is also hydrogen bonded to the side-chain carbonyl oxygen of N285 (Fig. 2Go). Because of the potential presence of water in the active site of CK during catalysis, we were concerned that mutation of N285 might lead to a pronounced increase in ATPase activity for the mutants, especially in the N285D mutant, where a general base would be introduced to make any water present more nucleophilic. The data reported in Table 2Go suggest that mutation of N285, in addition to significantly reducing the kinase activity, also reduces the ATPase activity of each mutant, although not proportionally as much as the kinase activity. Interestingly, the N285D mutant has the lowest ATPase activity of the three mutants. The ATPase activity of the N285Q mutant, which is the highest of the three mutants, is still only 0.018% of its kinase activity.

Milner-White and Watts (1971) were the first to propose that CK forms a quaternary CK•MgADP•nitrate•creatine TSAC in which nitrate mimics the planar {gamma}-phosphate in the transition state for transfer between the nucleotide and guanidino substrates. This was subsequently confirmed by spectroscopic (Reed and Cohn 1972; Reed and Leyh 1980) and x-ray crystallographic (Zhou et al. 1998) studies. We recently showed, using the quenching of the intrinsic CK tryptophan fluorescence by added nucleotide, that the simultaneous presence of creatine and nitrate lowers the apparent Kd for MgADP and promotes the formation of a quaternary creatine•nitrate•MgADP•CK TSAC (Borders, Jr. et al. 2002). Similar experiments on the N285 mutants show that a similar enhancement of MgADP affinity by creatine/nitrate does not occur (Table 3Go), suggesting that these N285 mutants do not have the ability to form a quaternary TSAC. A second line of evidence for the formation of a TSAC is the significant increase in {Delta}%F on the formation of a TSAC with native CK (Table 3Go; Borders, Jr. et al. 2002). A likely explanation of this increase (Borders, Jr. et al. 2002) is that the fixation of nitrate, a known quencher of indole fluorescence (Steiner and Kirby 1969), near the tryptohan 227 fluorophore (Gross et al. 1994) further increases the quenching that occurs when nucleotide binds. We note that none of the N285 mutants show an enhancement in {Delta}%F in the presence of creatine and nitrate, relative to {Delta}%F in the absence of either or both of these species (Table 3Go), and we propose that this is still further evidence that the N285Q, N285A, and N285D mutants of CK lack the ability to form a TSAC comparable to that formed by the native enzyme.

The extent of fluorophore quenching in a static quenching experiment, that is, one in which the fluorescing species and quencher form a reversible complex, is dependent on a number of factors. These factors include, but are not restricted to, the distance between the fluorophore and quencher, the orientation of the two, and the polarity of the medium around the fluorophore (Lakowicz 1999). The data reported in Table 3Go show that MgADP saturates native recombinant CK in the absence of added creatine and nitrate with a {Delta}%F of approximately 15%, whereas the corresponding value for each N285 mutant is significantly higher—21% for N285A, 23% for N285D, and 29% for N285Q. A similar trend is seen when either creatine or nitrate is present during titration, but not when both are present, for the reasons outlined above. We propose that even though each of the N285 mutants binds MgADP with an affinity that is the same or only slightly higher than the native enzyme, the environment of the bound nucleotide is noticeably different in the mutant CKs than in native CK.


    Conclusion
 TOP
 Abstract
 Introduction
 Results
 Discussion
 Conclusion
 Materials and methods
 References
 
The data reported herein strongly support the possibility that asparagine 285 plays a key role in transition-state stabilization in the reaction catalyzed by CK. Kinetic analysis of the N285Q, N285A, and N285D mutants shows that the major contributor to the approximately 104 reduction of catalytic efficiency of each mutant compared to the native enzyme is a reduction in kcat relative to the native enzyme. This is especially true of the N285D mutant, where isosteric replacement of the asparagine side chain by aspartate leads to a 5000-fold reduction in kcat, but almost no change occurs in the KM value for each substrate. Thus substrate binding affinity is unaltered, but catalytic efficiency is greatly reduced. A likely explanation is that the alignment of substrates at the active sites of the mutants is altered to the point that the activation barrier for phosphate transfer is much higher. The N285A mutant was altered to the point that the only reasonable fit of the kinetic data is to an ordered binding mechanism. Unlike the native CK, where the simultaneous presence of creatine and nitrate lowers the apparent Kd for MgADP approximately 10-fold due to the formation of a TSAC, the N285 mutants display no evidence of TSAC formation. We conclude that asparagine 285 plays a major role in transition-state stabilization in the reaction catalyzed by CK.


    Materials and methods
 TOP
 Abstract
 Introduction
 Results
 Discussion
 Conclusion
 Materials and methods
 References
 
Materials
The 4423-bp pET17b/CK7 construct used for site-directed mutagenesis is described elsewhere (Chen et al. 1996). Chemicals and reagents used for enzyme purification, kinetic analysis, and fluorescence measurements were obtained from Sigma, Fisher, or J.T. Baker and are described elsewhere (Edmiston et al. 2001; Borders, Jr. et al. 2002), as are the molecular biology reagents and procedures used for mutagenesis (Edmiston et al. 2001).

Procedures
Site-directed mutagenesis and enzyme purification and characterization were carried out by published procedures (Edmiston et al. 2001). Fluorescence measurements were made at 30.0 ± 0.1°C as described (Borders, Jr. et al. 2002), using either an SLM Aminco 8100 spectrofluorometer or an ISA JobinYvon-Spex FluoroMax-2 spectrofluorometer. The procedures used for data collection and correction, as well as data analysis to determine Kd(MgADP) and {Delta}%F under different experimental conditions, are described elsewhere (Borders, Jr., et al. 2002).

Creatine kinase activity
CK activity was determined at 30.0°C in the direction of phosphocreatine formation using a pH-Stat method as described (Edmiston et al. 2001). The data were analyzed for random-order, rapid-equilibrium. or ordered binding mechanisms by the method of Cleland (1979), using software written by Dr. Ronald E. Viola (University of Toledo, Toledo, Ohio, USA).

ATPase activity
The assay for ATPase activity was adapted from a published procedure (LeBel et al. 1978). The method involves a colorimetric assay of inorganic phosphate released during ATP hydrolysis, based on the reduction of the phosphomolybdate complex by 4-methylaminophenol sulfate. Each assay was carried out at 30°C and pH 9.00 in a 1.00-mL reaction mixture containing 0.1 M glycine, 6.0 mM magnesium acetate, 1.00 mM ATP, and 6.0 mg CK (wild-type or mutant). Blanks contained all components except the enzyme. At four appropriate time intervals, 200-µL aliquots from each assay were mixed with an equal volume of 10% trichloroacetic acid to precipitate the enzyme. After centrifugation at 14,000 rpm and 4°C for 10 min to remove insoluble materials, 200 µL of the supernatant was added to a mixture of 600 µL of 0.16% CuSO4 in 2.78% sodium acetate, 2 M acetic acid, pH 4.0, and 100 µL of 5% ammonium molybdate. After thorough mixing, 100 µL of 2.0% 4-methylaminophenol sulfate in 5.0% Na2CO3 was added, and the solution was stored on ice for 60 min before determination of the absorbance at 870 nm. After correction for the blank at each assay time, the inorganic phosphate concentration of each quenched sample was determined from a standard curve. The four data points for each assay were plotted to determine µmole phosphate/min, and this value was divided by the amount of CK in each assay to give the specific ATPase activity.


    Acknowledgments
 
This work was supported by NSF Grant 9982401 (C.L.B. and P.L.E.), Scholar/Fellow Award SF-96-001 from the Camille and Henry Dreyfus Foundation (C.L.B. and P.L.E.), and Research Corporation Grant CC4075 (C.L.B.). We thank Dr. Lorenzo H. Chen for advice in the early stages of this project; Drs. Richard Wolfenden, Brian G. Miller, Ronald E. Viola, and Vern L. Schramm for helpful discussions and suggestions; Dr. Ashutosh Tripathy of the University of North Carolina Macromolecular Interactions Facility for help in the early stage of the fluorescence measurements; and Michael J. Jourden for help with some of the fluorescence quenching measurements.

The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.


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 Introduction
 Results
 Discussion
 Conclusion
 Materials and methods
 References
 
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