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J. Biol. Chem., Vol. 277, Issue 42, 39548-39553, October 18, 2002
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,From the Department of Molecular Biology and Pharmacology and the Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
Received for publication, August 6, 2002
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ABSTRACT |
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The inhibition of Escherichia coli
D-3-phosphoglycerate dehydrogenase by L-serine
is positively cooperative with a Hill coefficient of ~2, whereas the
binding of the inhibitor, L-serine, to the apoenzyme
displays positive cooperativity in the binding of the first two serine
molecules and negative cooperativity in the binding of the last two
serine molecules. An earlier report demonstrated that the presence of
phosphate appeared to lessen the degree of both the positive and
negative cooperativity, but the cause of this effect was unknown. This
study demonstrates that the presence of intrinsically bound NADH was
responsible to a substantial degree for this effect. In addition, this
study also provides evidence for negative cooperativity in NADH binding
and for at least two NADH-induced conformational forms of the enzyme
that bind the inhibitor in the physiological range. Successive binding
of NADH to the enzyme resulted in an increase in the affinity for the first inhibitor ligand bound and a lessening of both the positive and
negative cooperativity of inhibitor binding as compared with that seen
in the absence of NADH. This effect was specific for NADH and was not
observed in the presence of NAD+ or the substrate
D-3-Phosphoglycerate dehydrogenase (PGDH, EC
1.1.1.95)1 from
Escherichia coli catalyzes the first committed step in the
phosphorylated pathway of L-serine biosynthesis. In turn,
L-serine inhibits PGDH catalytic activity in an
allosteric, cooperative manner (1-3). PGDH is a homo-tetrameric enzyme
that contains four active sites and four L-serine binding
sites (4). The binding of L-serine to PGDH has been studied
and shown to exhibit characteristics of both positive and negative
cooperativity (5). L-Serine binds to PGDH at the interface
between two adjacent regulatory domains with two molecules of
L-serine binding at each of the two regulatory domain
interfaces (4). Each serine molecule forms hydrogen bonds with adjacent
domains forming a hydrogen bond network across the non-covalent
interface. This network appears to tether the domains together and
results in inhibition of catalytic activity (4, 6). It has been
proposed that the potential binding of two effector molecules at a
single interface could explain the negative cooperativity of ligand
binding if a single effector molecule was capable of stabilizing the
association of the two domains (5) to the extent that it could exclude,
or partially exclude, the binding of the second ligand.
L-serine binding was shown to display
significant differences in binding behavior in the presence of
phosphate (7). This manifested itself in an alteration of the degree of
both the positive and negative cooperativity of serine binding as well
as the relative sensitivity of PGDH to serine concentration. This
effect seemed to be unique to phosphate among the buffers tested in
that several other buffers acted similarly to each other but
differently from phosphate. The nature of this "phosphate effect"
was unknown at the time, but it was proposed that the phosphate ion
might interact at the active site since phosphate groups are part of
the natural substrates, 3-phosphoglycerate and NAD+ (7). It
was suggested that linkage between the active sites and the serine
binding sites could result in a more open form of the regulatory
interface in response to phosphate interaction at the active site,
which might then manifest itself in a greater ease of serine binding
and a lessening of cooperative effects.
If this phosphate effect is the result of interaction at the
active site, it suggests that the natural substrates of the enzyme, which contain phosphate groups, would also have a measurable effect on
the serine binding characteristics. Such reciprocal effects, that is,
the binding of ligand at one site affecting the binding of another
ligand at a separate site, is not uncommon (8). In fact, this is
essentially the basis for K-type regulation in allosteric systems
(8).
PGDH has been reported to be basically a V-type regulatory
system (2). In other words, binding of effector has its major effect on
the velocity of the enzyme rather than on substrate binding. In this
respect and in light of recent observations (7), it was of interest to
explore the potential significance of this further.
Sugimoto and Pizer (1) reported that purified PGDH contained
approximately two molecules of intrinsically bound NADH. The amount of
NADH bound could be observed by fluorescence resonance energy transfer
between tryptophan residues in the enzyme and the bound NADH (1).
Sugimoto and Pizer (1) also reported that the fluorescence signal due
to bound NADH was affected by the presence of L-serine, but
they concluded that serine only altered the fluorescence properties of
the enzyme rather than the amount of bound NADH.
To further explore the modulation of cooperativity in PGDH, the effect
of cofactors and substrates on the L-serine binding characteristics of PGDH were investigated. This report provides evidence that although some effect of phosphate buffer is seen, a major
effect on serine binding is the direct influence of the binding of NADH
but not of NAD+ or PGDH was produced and isolated as described previously (9, 10).
All experiments were performed with PGDH 4C/A, which is a
form of the enzyme in which the 4 cysteine residues in each subunit are
converted to alanine residues (11). After cell lysis and ammonium
sulfate fractionation, the enzyme was purified by affinity
chromatography on a column of 5'-AMP-Sepharose and eluted with NADH.
After elution, the enzyme was dialyzed directly against either 20 mM potassium phosphate buffer, pH 7.5, 1 mM DTT, 1 mM EDTA or 20 mM Tris
buffer, pH 7.5, 1 mM DTT, 1 mM EDTA. In
some instances, as described below, the NADH was converted to
NAD+ by the addition of Serine binding was measured by equilibrium dialysis in 200-µl
dialysis chambers (Sialomed, Inc., Columbia, MD) purchased from the
Nest Group (Southborough, MA). Dialysis was performed for 16 h
with [3H]L-serine in appropriate
concentrations of unlabeled L-serine. Cells were sampled in
triplicate, and the average of 10-min counts was used to calculate
concentrations of free and bound L-serine. The nominal PGDH
concentration was 5-10 µM tetramer in all binding experiments. When indicated, NADH, NAD+, and
Fluorescence experiments were performed on a PerkinElmer Life
Sciences LS-50B luminescence spectrometer. NADH binding was determined
under conditions for stoichiometric binding, which is defined as a
concentration of the acceptor that is at least 10 times greater than
the dissociation constant of the ligand (15). Excitation was performed
at 295 nm, and emission was monitored at 420 nm (1). Fluorescence
intensity was corrected for dilution. As NADH binds to protein, the
F420 rises in response to the resonance energy transfer.
After the enzyme is saturated with ligand, the remaining increase in
F420 is due to free NADH in solution. Extrapolation of the
slopes of these two responses gives the moles of NADH bound per moles
of tetrameric PGDH at their point of intersection (15). When indicated,
L-serine was present at a concentration of 200 µM. Fluorescence scans were performed with excitation at
295 nm and emission monitored from 300 to 450 nm. NADH concentration was determined by absorbance at 340 nm using a molar extinction coefficient of 6.22 × 103 (16).
Fig. 1 shows the fluorescence
spectrum of PGDH after isolation from a 5'-AMP-Sepharose affinity
column followed by dialysis to remove free NADH. The fluorescence at
420 nm is an indication of the amount of NADH bound to the
enzyme. Also shown is the spectrum of PGDH after it has been
treated with the substrate
-ketoglutarate. Conversely, the binding of L-serine did
not have a significant effect on the stoichiometry of NADH binding,
consistent with it being a V-type allosteric system. Thus,
cofactor-related conditions were found in equilibrium binding
experiments that significantly altered the cooperativity of inhibitor
binding. Since the result of inhibitor binding is a reduction in the
catalytic activity, the binding of inhibitor to these NADH-induced
conformers must also induce additional conformations that lead to
differential inhibition of catalytic activity.
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INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES
-ketoglutarate.
![]()
MATERIALS AND METHODS
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES
-ketoglutarate prior to
dialysis. This conversion was monitored by following the fluorescence
of the solution at 420 nm as described below. Catalytic activity was
monitored by the change in absorbance at 340 nm due to the conversion
of NADH to NAD+ at pH 7.5 (12) using
-ketoglutarate as
the substrate (13). Protein concentration was determined by
quantitative amino acid analysis.
-ketoglutarate were present in solution at 100 µM, 100 µM, and 5 mM, respectively. The dissociation
constants reported for NADH and NAD+ are 0.05 and 8 µM, respectively (1), and the Km for
-ketoglutarate is 0.3 mM. Serine binding data were fit
to the Adair equation for four binding sites using Kaleidograph
(Synergy Software) as described previously (5, 14).
![]()
RESULTS
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES
-ketoglutarate. Titration of the sample
containing intrinsically bound NADH with additional NADH (Fig.
2) produces an increase in the
fluorescence at 420 nm, which corresponds to the binding of ~2
additional NADH per tetramer, which is consistent with there being ~2
mol of NADH bound/tetramer in the isolated enzyme.

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Fig. 1.
Fluorescence spectra of
PGDH. a, immediately after purification, PGDH was
dialyzed in 20 mM potassium phosphate buffer, pH 7.5, 1 mM DTT, 1 mM EDTA for 18 h and scanned
after a 20-fold dilution in the same buffer; b, scan of the
same sample 5 min after the addition of 1 µl of 10 mg/ml
-ketoglutarate. INT, intensity, solid
line.

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Fig. 2.
Fluorescence titration of PGDH containing
intrinsically bound NADH. Immediately after purification, PGDH was
dialyzed against Tris or phosphate buffer and then titrated with
NADH in the same buffer. The y axis is expressed as the
fluorescence at 420 nm minus the initial fluorescence before addition
of NADH, F-Fo. The x axis is
expressed as moles of NADH per moles of protein (tetramer). Solid
lines are extrapolations of the initial and final slopes, and
dashed lines are extrapolations of the slope intersections
to the x axis.
, 20 mM potassium phosphate
buffer, pH 7.5, 1 mM DTT, 1 mM EDTA;
, 20 mM Tris-HCl, pH 7.5, 1 mM DTT, 1 mM
EDTA.
Treatment of PGDH containing intrinsically bound NADH with
-ketoglutarate results in a decrease of the signal at 420 nm due to
the conversion of bound NADH to NAD+ (Fig. 1). After
dialysis, samples titrated with NADH (Figs.
3 and 4) show that they are capable of
binding ~4 NADH/tetramer. Thus, the
NAD+ produced by reaction
with
-ketoglutarate either dissociates from the enzyme during
dialysis or can be freely displaced by NADH if it is still bound to the
enzyme.
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It was reported previously that binding of L-serine to PGDH
in phosphate buffer appeared to exhibit a lesser degree of
cooperativity than binding in Tris buffer (5, 7). However, this was
done without prior removal of intrinsically bound NADH. To explore this
further, serine binding was performed with enzyme that was depleted of
NADH and dialyzed with phosphate buffer. The binding curves measured in
the absence and presence of saturating levels of NADH,
NAD+, and
-ketoglutarate are shown in Fig.
5. The binding parameters derived from
fitting the data to the Adair equation are shown in Table
I. Serine binding to PGDH in the presence
of saturating NADH reduces both the positive and negative
cooperativity of binding as compared with binding in phosphate in the
absence of NADH or in the presence of NAD+ or
-ketoglutarate. The binding in phosphate in the presence of NADH
from this study is similar to the binding in phosphate reported
previously (7) in that the degree of apparent positive cooperativity is
decreased and the binding of the fourth ligand is now measurable. The
effect of NADH on serine binding in Tris buffer shows similar behavior
in the lessening of positive cooperativity but not the negative
cooperativity (Fig. 6).
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Differential effects of NADH levels on the serine binding
characteristics of PGDH can also be observed. The Scatchard analyses in
Fig. 7 are derived under conditions in
which NADH is depleted from the enzyme, when only intrinsically bound
NADH remains on the enzyme (after dialysis), or when the enzyme is
saturated with NADH. The decrease in the concavity of the Scatchard
plots shows that the degree of cooperativity observed progressively
decreases as the NADH status progresses from complete absence to
saturation. As expected, the derived dissociation constants listed in
Table I show a distinct progression from no NADH to saturating
NADH.
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The distribution of each effector-bound species, calculated from the
Adair constants presented in Table I for PGDH in the absence and
presence of saturating NADH in phosphate buffer, is shown in Fig.
8. The nearly 6-fold increase in affinity
for the first inhibitor ligand in the presence of NADH significantly
enhances the inhibitor occupancy of PGDH at very low serine
concentrations. For instance, at 1 µM
L-serine, the percentage of enzyme with at least one
inhibitor ligand bound increases from ~16 to ~50% in the presence
of NADH. In addition, the species with at least three inhibitor ligands
bound is also significantly enhanced in the presence of NADH. At 5 µM L-serine, this occupancy increases from
about 5 to 27%, and at 10 µM L-serine, it
increases from 12 to 55%. The population of species with at least two
ligands bound is also increased in the presence of NADH but not nearly to the extent as the others.
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Because of the effect that the presence of NADH has on
serine binding, the effect of serine on NADH binding was also
investigated. NADH titrations of NADH-depleted PGDH in the presence of
saturating levels of L-serine (Figs. 3 and 4) demonstrate
that serine has no appreciable effect on the level of NADH binding in
either Tris or phosphate buffer. Serine did appear to enhance the
fluorescence slightly in phosphate buffer (Fig. 3), but the number of
NADH molecules bound was not altered.
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DISCUSSION |
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We reported previously (7) that phosphate buffer appeared to have a specific effect on the binding of serine to PGDH that was not evident with other buffers such as Tris, imidazole, and borate. The results of the studies reported here show that the presence of bound NADH also exhibits a significant effect on the binding of L-serine. Furthermore, this effect is specific for the reduced cofactor since it is not observed with NAD+.
The data in Table I, which were derived from the serine binding curves,
show that phosphate buffer alone (phosphate
NADH) may
slightly reduce the level of positive cooperativity in the binding of
the first two ligands as compared with Tris buffer. However, phosphate
alone does not appear to alter the negative cooperativity in the
binding of subsequent serine ligands. Serine binding in phosphate
buffer in the presence of either NAD+ or
-ketoglutarate
produces very similar binding parameters to that of phosphate alone
(phosphate
NADH). It is not until NADH is introduced into the
solution that a significant increase in the affinity of the first
ligand and a decrease in the negative cooperativity are seen. In regard
to the latter, the presence of NADH now brings binding of the last
ligand into the measurable range, whereas under all other conditions,
binding is too weak to measure. Note that this does not happen in Tris
buffer in the presence of NADH. This is consistent with the previous
report (7) since no effort was made to remove the bound NADH from the
protein used in those studies. Therefore, these results indicate that
the phosphate effect reported previously (7) appears to be due to a
combination of effects from the phosphate ion as well as bound NADH.
On the other hand, the ability of PGDH to bind NADH does not appear to be affected by the level of L-serine. This is consistent with the early work of Sugimoto and Pizer (1), who concluded that serine altered the fluorescent properties of the enzyme rather than the amount of NADH bound.
It is difficult to assess the physiologic significance of the effect of NADH since comparable binding parameters are not obtainable when the enzyme is actively turning over substrate and cofactor. It is well known, however, that serine inhibits activity in a cooperative manner during catalysis in vitro in either the direction of NADH oxidation or reduction (2) but with a 10-fold higher sensitivity to serine in the direction of NADH oxidation. Physiologically, the reaction catalyzed by PGDH proceeds in the direction of reduction of NAD+, although the equilibrium of the reaction in the test tube lies well in the other direction (2). That the reaction functions as it does physiologically has been attributed to the depletion of the reaction products by the associated metabolism, thus drawing the reaction in the forward direction. This in itself would represent a level of control over the production of L-serine or the intermediate products of the pathway. That serine binding appears to be more positively cooperative in the physiological direction in which the enzyme binds NAD+ as a substrate suggests an additional potential for fine-tuning in the level of control. However, Dubrow and Pizer (17) have presented pre-steady state kinetic evidence that suggested that PGDH is not in the same conformation in the enzyme-reduced cofactor complex as it is when it is turning over.
Although these data show a change in effector binding characteristics in response to cofactor, it is difficult to explain the inhibition characteristics in terms of the effector binding pattern alone. Moreover, additional changes in effector binding may occur when both substrate and cofactor are interacting with the enzyme. Thus, care must be taken when trying to interpret the results of individual ligand binding experiments in the context of an enzyme that is actively turning over, especially when conclusions regarding comparative stoichiometry are made.
PGDH has been classified as a V-type enzyme (2), meaning that
regulation of activity is basically through modulation of the catalytic
turnover rate rather than substrate binding, which is the case
for K-type enzymes. The present studies are consistent with this
conclusion, but somewhat unexpected is the significant effect of
cofactor binding on effector binding without a similar effect in the
opposite direction. The differential binding of NADH visualized in Fig.
7, as well as in Figs. 2 and 3, provides evidence for at least two
additional conformational states of the protein. These two additional
states correspond to enzyme with intrinsically bound NADH and enzyme
under conditions of saturating NADH. This observation has at least two
implications. First, the enzyme displays negative cooperativity in the
binding of NADH. Two sites in the enzyme bind NADH very tightly since
enzyme is purified with two NADH molecules bound/tetramer, which do not dissociate during dialysis. Second, in the presence of additional NADH,
the last two sites bind NADH with weaker affinity. This observation is
not unprecedented for dehydrogenases which bind NADH as a cofactor. For
instance, glyceraldehyde-3 phosphate dehydrogenase from rabbit muscle
(18) displays increasing dissociation constants for the four sites that
range from around 10
11 for the first site to
10
5 for the last site.
Consistent with the induced fit theory of Koshland et al. (19), this study presents evidence for at least three different states that bind inhibitor with affinities in the physiological range that clearly differ in their individual site affinity for the inhibitor. One state exists in the absence of NADH binding, and the latter two are induced by NADH binding. The two induced states manifest themselves most strikingly in an increase in affinity for the first ligand to bind and an increase in the overall degree of ligand binding. In addition, there is a progressive loss of cooperative behavior of effector binding as cofactor occupancy increases. Thus, in addition to the negative cooperativity that cannot be accommodated by the Monod model (8), these data are also more consistent with some variation of the Koshland model, which states that the conformation of each subunit changes in turn as it binds ligand. Furthermore, in addition to the multiple states induced by NADH binding, the subsequent binding to these states by the inhibitor, L-serine, must also induce at least one, and probably more, conformational states that lead to inhibition of catalytic activity.
Previously, we have shown that mutations in hinge areas between the
inhibitor binding domain and the active site can actually uncouple the
cooperativity of inhibition from the cooperativity of serine binding
(14, 20, 21). If these mutations literally interrupt the flow of
conformational information between these two distant sites because of
mutations that hinder movement around these hinges, then one might
expect them to also interrupt the effect of NADH on inhibitor binding.
However, if the mechanisms for these two phenomena are not the same,
then a different outcome would be expected. Investigations are now
ongoing to test this hypothesis. In either case, these investigations
will provide additional insight into the structural basis for the
cooperative allosteric regulation of this enzyme.
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FOOTNOTES |
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* This work was supported by Grant GM 56676 from the National Institutes of Health.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
To whom correspondence should be addressed: Dept. of Molecular
Biology and Pharmacology, Box 8103, Washington University School of
Medicine, 660 S. Euclid Ave., St. Louis, MO 63110. Tel.: 314-362-3367; Fax: 314-362-4698; E-mail: ggrant@pcg.wustl.edu.
Published, JBC Papers in Press, August 14, 2002, DOI 10.1074/jbc.M208019200
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ABBREVIATIONS |
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The abbreviations used are: PGDH, D-3-phosphoglycerate dehydrogenase; DTT, dithiothreitol.
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REFERENCES |
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