(Received for publication, March 20, 1997, and in revised form, April 29, 1997)
From the Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011
Gln34, Gln224, Leu228, and Ser240 are conserved residues in the vicinity of bound IMP in the crystal structure of Escherichia coli adenylosuccinate synthetase. Directed mutations were carried out, and wild-type and mutant enzymes were purified to homogeneity. Circular dichroism spectroscopy indicated no difference in secondary structure between the mutants and the wild-type enzyme in the absence of substrates. Mutants L228A and S240A exhibited modest changes in their initial rate kinetics relative to the wild-type enzyme, suggesting that neither Leu228 nor Ser240 play essential roles in substrate binding or catalysis. The mutants Q224M and Q224E exhibited no significant change in KmGTP and KmASP and modest changes in KmIMP relative to the wild-type enzyme. However, kcat decreased 13-fold for the Q224M mutant and 104-fold for the Q224E mutant relative to the wild-type enzyme. Furthermore, the Q224E mutant showed an optimum pH at 6.2, which is 1.5 pH units lower than that of the wild-type enzyme. Tryptophan emission fluorescence spectra of Q224M, Q224E, and wild-type proteins under denaturing conditions indicate comparable stabilities. Mutant Q34E exhibits a 60-fold decrease in kcat compared with that of the wild-type enzyme, which is attributed to the disruption of the Gln34 to Gln224 hydrogen bond observed in crystal structures. Presented here is a mechanism for the synthetase, whereby Gln224 works in concert with Asp13 to stabilize the 6-oxyanion of IMP.
Adenylosuccinate synthetase (IMP:L-aspartate ligase (GTP-forming), EC 6.3.4.4, AMPSase)1 catalyzes the first committed step in de novo AMP synthesis, using GTP as the energy source to couple IMP and aspartate (1). The synthetase is the target of a natural herbicide (2-5), and the enzyme is a potential target in the development of drugs against human immunodeficiency virus or cancer (6).
Known primary sequences of AMPSase, including those of bacteria and mammals (7-15) are 40-90% identical, implying similar structure and function for this protein, regardless of source. Crystal structures of Escherichia coli AMPSase in its ligand-free state (16, 17) and its ligated state (4, 18-20) are in the literature.
The chemical mechanism proposed for the synthetase by Lieberman (21)
and Fromm (22) calls for the formation of 6-phosphoryl-IMP (19, 23, 24)
as an intermediate in the catalytic reaction. O-6 of IMP putatively
makes a nucleophilic attack on the -phosphorus atom of GTP,
whereupon the amino group of L-aspartate (ASP) displaces phosphate from C-6 of the intermediate. The direct observation of
6-thiophosphoryl-IMP in the active site of the synthetase (20) provides
additional support for the proposed mechanism, which, on the basis of
initial rate kinetics, is rapid equilibrium random ter ter (25).
Isotope exchange studies with the rat muscle enzyme imply a preferred
pathway for substrate addition, with aspartate adding to the enzyme
after the binding of nucleotides (24). Competitive inhibitors for one
of the substrates inhibit noncompetitively with respect to the other
two substrates, suggesting that substrate binding sites do not overlap
(Ref. 1 and references therein). Furthermore, adenylosuccinate (AMPS)
is a competitive inhibitor of IMP and a noncompetitive inhibitor of GTP
and ASP, a result consistent with overlapping AMPS and IMP binding
sites (25).
Residues located in the vicinity of C-6 of IMP should be important in
catalysis and/or substrate binding. Directed mutation, kinetics, and
molecular modeling (19, 26) revealed the significance of
Arg305 to the recognition of ASP and the stabilization of
the transition state. The putative binding of Arg305 to the
-carboxylate of ASP may bring the amino group of ASP into close
contact with C-6 of IMP (19). However, Arg305 is probably
not a significant factor in the formation of 6-phosphoryl-IMP. Positions corresponding to 224 are occupied either by Gln or Asn in 12 of the 13 known sequences of AMPSase. The side chain of Gln224 hydrogen bonds to N-7 and O-6 of IMP (19). On the
basis of results presented below, Gln224 is essential for
catalysis. Furthermore, the mutation of Gln34 to glutamate
causes a 60-fold decline in kcat, attributed to the disruption of a hydrogen bond between Gln34 and
Gln224, that was observed in ligated crystal structures
(19). In contrast, alanine mutations of Leu228 and
Ser240, which are conserved residues near bound IMP, had
little effect on the kinetics of the synthetase.
GTP, IMP, L-aspartate,
adenylosuccinate, phenylmethylsulfonyl fluoride, and bovine serum
albumin were obtained from Sigma. A site-directed mutagenesis kit was
obtained from Amersham Corp. Restriction enzymes were obtained from
Promega. E. coli strain XL-1 blue was obtained from
Stratagene. An E. coli purA strain H1238
(thr-25, tonA49, argF58, purA54, argI61) and an E. coli purB
strain H680 (fhuA2, lacY1, tsx-70,
glnV44(AS), gal-6,
-, purB51, trpC45, his-68, tyrA2, rspL125(strR),
malT1(
R), xylA7, mtlA2, thi-1) were
obtained from Dr. B. Bachman, Genetic Center, Yale University.
0.45-µm polyvinylidene difluoride membranes were obtained from
Millipore Corp. Other reagents and chemicals were obtained from
Sigma.
Recombinant DNA manipulation
employed standard procedures (27). The plasmid containing a
1.8-kilobase pair BamHI-HindIII fragment from
PMS204, ligated into PUC118, was used in mutagenesis. The mutagenesis
primers were as follows: 5-tgaccgccctcgtagcgtacaa-3
for
Q34E, 5
-atccagcagcgtacccatcgcaccttc-3
for Q224M,
5
-atccagcagcgtaccctccgcaccttc-3
for Q224E,
5
-gatatccagcgccagcgtacc-3
for L228A, and
5
-gtgttggaagcagttacgtacg-3
for S240A. The underlined
bases are changes from the original sequence. The primers used to
sequence DNA in the vicinity of residues 224-240 and 34 are
5
-ATGGCTGTTGCCGACATC-3
and 5
-GACGAAGGTAAAGGTAAG-3
, respectively.
All primers were synthesized on a Bioresearch 8570EX automated DNA
synthesizer at the nucleic acids facility at Iowa State University.
Mutagenesis was carried out according to the protocol provided by
Amersham. The mutations were confirmed by DNA sequencing using the
chain termination method (28) at the nucleic acids facility. The
1.8-kilobase pair BamHI-HindIII fragment with the
right mutation was ligated back into PMS204, which was used in the
transformation of XL-1 blue cells. The plasmids isolated from that
strain were used to transform E. coli purA
H1238, the strain used for protein expression.
Protein concentration, defined in terms of monomers, was determined by the method of Bradford (29), using bovine serum albumin as the standard. Molecular mass was determined by matrix-assisted laser desorption/ionization time of flight mass spectroscopy (30).
Purification of Wild-type and Mutant AMPSaseThe wild-type and mutant enzymes were purified using ammonium sulfate precipitation, phenyl-Sepharose CL-4B chromatography, Cibacron blue affinity chromatography, and DEAE-TSK high pressure liquid chromatography, as described elsewhere (31, 32), but subject to the following modifications. Enzyme was eluted from a phenyl-Sepharose CL-4B column by a series of potassium phosphate-buffered solutions: 0.6 M, 0.4 M, and 0.2 M (NH4)2SO4 in 50 mM potassium phosphate (pH 7.0). The wild-type and most of the mutant enzymes appeared in the 0.2 M (NH4)2SO4 solution. A large fraction (80%) of the Q224E mutant, however, appeared in the 0.4 M (NH4)2SO4 solution. Enzyme purity was monitored by SDS-PAGE (33).
Western BlotBecause of the slower growth rate of transformed cells and the elevated expression of the Q224E mutant relative to the wild-type enzyme, we performed Western blots on wild-type, Q224M, and Q224E AMPSases to verify that our isolated mutant enzymes were indeed modifications of AMPSase. Two sets of 0.5 µg of Q224M, Q224E, and wild-type AMPSases and 1 µg of adenylosuccinate lyase (AMPS lyase) were separated by electrophoresis on a 12% SDS-polyacrylamide gel and then transferred to a polyvinylidene difluoride membrane. A rabbit polyclonal antibody (1:5000) and the standard detection techniques (AuroProbe BLPlus and intenSE BL system, Amersham) were used to visualize the signals.
Coupled Assay MethodUV difference spectra were obtained on
a GBC UV/VIS 918 spectrophotometer equipped with a Peltier-Effect
temperature controller, using the program Scan from 300 to 220 nm.
The reaction buffer contained 20 mM Hepes (pH 7.7), 300 µM GTP, 450 µM IMP, 5 mM
MgCl2, 5 mM ASP, and excess AMPS lyase. 1 µg/ml wild-type AMPSase or 300 µg/ml Q224E mutant enzyme was used
in the scan. The spectra obtained at time 0 were subtracted from the
spectra collected at subsequent time points (Fig.
1).
A coupled assay method monitoring the production of AMP employed UV
difference spectroscopy. Excess AMPS lyase was used in the reaction
mixture to convert all the AMPS into AMP. The increase in absorbance at
275 nm was monitored using a = 15.0 × 106
cm2/mol, which was derived by comparing the
kcat values for wild-type enzyme using the assay
method described elsewhere (34) and the method developed in this
study.
The concentrations of stock solutions for GTP and IMP were determined using their extinction coefficients at 253 and 248 nm, respectively. Enzyme assays contained 20 mM Hepes (pH 7.7), and 5 mM MgCl2. When GTP was the variable substrate, ASP was fixed at 5 mM, and IMP was fixed at 450 µM. When IMP was the variable substrate, GTP was fixed at 300 µM, and ASP was fixed at 5 mM. When ASP was the variable substrate, GTP was fixed at 300 µM, and IMP was fixed at 450 µM.
Circular Dichroism SpectrometryCircular dichroism spectra for the wild-type enzyme and the mutant enzymes were acquired on a JASCO J700. Samples (100 µg/ml) were placed in a 1-cm cuvette, and data were collected in increments of 0.1 nm. Each spectrum was corrected for background contributions of the buffer and smoothed. The data were analyzed by software associated with the spectrometer or by PSIPLOT.
Intrinsic Tryptophan Emission Fluorescence MeasurementsFluorescence measurements, using 1-cm quartz cuvettes, were carried out in a SLM 8000C spectrofluorometer. The proteins were excited at 290 nm, and emission spectra were recorded from 300 to 400 nm. Each sample contained 200 µg/ml protein in 20 mM Hepes buffer (pH 7.7). Solutions containing 0-1.5 N guanidium hydrochloride were used in denaturation experiments.
pH-dependent Kineticskcat versus pH profiles for the wild-type and the Q224E mutant were studied to gain additional data relevant to our proposals regarding the catalytic mechanism of the synthetase and the role in that mechanism played by the side chain at position 224. Mes and Hepes were chosen as buffers for the pH range 5.5-8.5, where the wild-type enzyme is active. The assay solution contained 300 µM GTP, 5 mM MgCl2, 5 mM ASP, and 20 mM Mes/Hepes buffer at different pH values. IMP concentrations varied from 25 to 500 µM. 300 µg/ml Q224E mutant or 1 µg/ml wild-type AMPSase with excess AMPS lyase were used in the assays. Longer assay times (5-10 min) compensated for the lower activity of the Q224E mutant enzyme.
Sequences of AMPSase
from different sources were aligned using the PILEUP option of the GCG
sequence analysis package. Positions equivalent to 224 are occupied by
asparagine in four sequences, glutamine in eight sequences, and
arginine in the AMPSase from Brucella abortus, suggesting a
significant role for the amide side chain at this position (Table
I). Indeed, Gln224 hydrogen bonds to the
6-oxo and N-7 of IMP in a crystal structure of the ligated synthetase
(19). Position 34 is occupied by glutamine in 10 of 13 sequences. In
ligated crystal structures of the E. coli enzyme, NE2 of
Gln34 hydrogen bonds to OE1 of Gln224, properly
orienting the amide side chain of Gln224 with respect to
bound IMP (Fig. 2). Positions 228 and 240 are leucine
and serine, respectively, in all known sequences of the synthetase. The
side chain of Leu228 packs against the base of IMP,
whereas OG of Ser240 hydrogen bonds to the 5-phosphoryl
group of IMP by way of a bridging water molecule.
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Mutagenesis, Expression, and Purification of AMPS Synthetases
All the enzymes reported in this study exhibited
greater than 95% purity by SDS-polyacrylamide gel electrophoresis. The
molecular mass of the synthetase by matrix-assisted laser
desorption/ionization time of flight mass spectroscopy was 46 kDa,
consistent with the calculated molecular mass of its polypeptide chain.
Q224E grew much slower on LB agar plates and in liquid media. Cultures
yielded a cell mass of 1.5 g/liter, one-third of that produced by the wild-type strain. However, the yield of purified AMPSase was 15 mg/g of
cells, a 15-fold increase relative to the wild-type strain. This
phenomenon of reduced cell mass and increased enzyme expression has not
been observed for any other mutant of AMPSase. No activity was detected
using the assay method of Rudolph and Fromm (25) or Kang and Fromm
(32). The isolated protein was identified as a mutant of AMPSase by
Western blot and complementation experiments using H680 and H1238 as
the recipient strains. The wild-type, Q224M, and Q224E enzymes were
recognized by the antibody for AMPSase, whereas AMPS lyase was not
(data not shown). In M9 minimal medium, the Q224M, and Q224E mutant
plasmids complemented adenine auxotrophy of
purA in H1238 but not
purB
in H680.
The CD spectra of the mutant and wild-type enzymes were superimposable (data not shown) from 200 to 260 nm. These observations indicated the absence of global conformational changes or the disruption of the secondary structure.
Kinetic Characterization of Wild-type and Mutant AMPSasesThe kinetic parameters for wild-type and mutant AMPSases were determined in pH 7.7 Hepes buffer (Table II). No significant change in the Km values for GTP or ASP was observed for Q224E or Q224M enzymes relative to the wild-type enzyme. The Q224M mutant displayed a 5-fold increase in KmIMP, and a 13-fold decrease in kcat relative to the wild-type enzyme. On the other hand, the Q224E mutant, with only marginal changes in Km for all three substrates, exhibited a decrease in kcat of 4 orders of magnitude relative to wild-type AMPSase. Specificity constants (kcat/Km) for the Q224M mutant decreased 16-, 75-, and 14-fold for GTP, IMP, and ASP, respectively, relative to the wild-type enzyme, compared with an almost 104-fold decrease for specificity constants of the Q224E mutant for all substrates. These findings implicate Gln224 not only in the recognition of IMP but also in a critical catalytic function. The catalytic role of Gln224 had not been recognized previously on the basis of ligated crystal structures, but it is in harmony with the suggestion of Poland et al. (19) that IMP binds to the active site as the 6-oxyanion (see below).
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The substitution of Gln34 with glutamate resulted in a 60-fold decrease in kcat. Atom N-E2 of Gln34 hydrogen bonds with O-E1 of Gln224, which putatively orients Gln224 in its interaction with IMP. The Q34E mutant may force a 180° rotation of the amide side chain of Gln224 (see below). However, in the case of the Q34E mutant, one cannot rule out other explanations for the observed loss of activity, since the KmGTP also increased 20-fold relative to the wild-type enzyme. Gln34 is about 10 Å away from the GTP site, suggesting a conformational change over a significant distance.
Alanine substitution of Leu228 and Ser240 resulted in 3.6- and 1.4-fold decreases in kcat, respectively, relative to the wild-type enzyme. The side chain of Leu228 may contribute to the proper orientation of the base of IMP; however, Ser240 apparently plays no significant role in the recognition of IMP or in catalysis.
Intrinsic Tryptophan Emission Fluorescence MeasurementsThe fluorescence emission spectra of the mutants, Q34E, Q224M, and Q224E, and the wild-type enzyme were collected in the presence of different concentrations of guanidium chloride. The emission maximum was 333 nm for the mutants and wild-type enzymes in the absence of guanidium chloride, and gradually shifted to 350 nm in the presence of increasing concentrations of guanidium chloride up to 1.5 N (data not shown). Mutations at residues 34 and 224, then, did not change protein stability in the presence of denaturants relative to the wild-type enzyme.
pH Effects on AMPSase ActivityActing as hydrogen donors or
acceptors, the amide side chains of glutamine and asparagine do not
ionize, whereas glutamate and aspartate may undergo ionization.
Replacing the amide group of Gln224 with a carboxylate
group resulted in a decrease in kcat of 4 orders
of magnitude, whereas substrate affinity, as measured by Km, underwent only a modest change. We decided to
study the pH-dependent kinetics for the wild-type and Q224E
mutant enzymes to correlate enzyme activity with the state of
protonation of Glu224. Titration curves for mutant and
wild-type enzyme are typically bell-shaped for kcat
versus pH profiles (Fig. 3).
KmIMP for mutant and wild-type
enzymes showed a maximum 2-fold change over the pH range 5.5-8.5. The
optimum pH for wild-type AMPSase is 7.7, and that for the Q224E mutant
is 6.2. At pH 6.2, only a 20-fold decrease in
kcat was observed for the Q224E mutant relative to the wild-type enzyme. Protonation of the side chain of
Glu224 may be responsible for the increase in relative
activity of the Q224E mutant as the pH decreases from 7.7 to 6.2. It is
not possible, however, to rule out the suggestion that mutation of
Gln224 to Glu results in a localized environmental change
that affects the pK value of another critical residue.
The properties of Q224M, Q224E, and Q34E mutants of AMPSase can be
understood in relation to the crystal structure of the IMP·NO3 complex (19). For the
wild-type enzyme (Fig. 4A), Asp13
and Gln224 putatively work in concert to stabilize the
6-oxyanion of IMP. Donor-acceptor distances between relevant atoms of
Gln34, Gln224, Asp13, and IMP are
consistent with the hydrogen bonding of Fig. 4A. Furthermore, a D13A mutant has no observed activity (35), consistent with its proposed role as a catalytic base.
The Q34E mutant could disrupt the hydrogen bond between Gln224 and O-6 of IMP by enforcing a conformational change on Gln224 (Fig. 4B). However, there is some uncertainty in this interpretation because the Q34E mutant has no effect on KmIMP but does significantly increase KmGTP. Thus, the decrease in kcat observed for the Q34E mutant may stem from conformational changes in addition to those represented in Fig. 4B.
As the Km values for substrates are not significantly perturbed by the mutation Q224M, the decrease in kcat most likely emanates from the loss of hydrogen bonds to N-7 and O-6 of IMP, the latter probably having the largest impact on catalysis (Fig. 4C). The greater reduction in kcat for the Q224E mutant than for the Q224M mutant may stem from the localization of a negative charge in proximity to O-6 of IMP (Fig. 4D). Partial restoration of activity at pH 6.2, then, is due putatively to the protonation of Glu224, which reforms the critical hydrogen bond to O-6 of IMP (Fig. 4D). The failure to restore the Q224E mutant to 100% of the wild-type enzyme activity at pH 6.2 may be a consequence of (i) tautomeric states that put the proton onto O-6 (Fig. 4E) and/or (ii) the absence of the N-7 to Gln224 hydrogen bond, an absence that may undermine the stability of the hydrogen bond between Glu224 and O-6 of IMP.
The physiological importance of Gln224 is supported further by the phenomenon of reduced cell proliferation in combination with enhanced protein expression for the mutant Q224E. Mutation of essential catalytic residues severely inhibits the growth of E. coli in the case of D13A and H41N mutants (35). The kinetic data imply that a disruption of the purine nucleotide pathway may impair the reproductive capacity of the organism. The enhanced level of expression of the Q224E mutant may be a self-rescuing strategy of E. coli, to compensate for the impaired AMPSase and to promote adenylate synthesis by the purine nucleotide salvage pathway. It is unclear, however, why this mechanism of recovery is not operative in the case of the D13A or H41N mutant. Perhaps these mutants of AMPSase impair adenylate biosynthesis so severely that E. coli cannot sustain transcription and translation processes for overproduction of a given protein.