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J. Biol. Chem., Vol. 277, Issue 13, 11450-11455, March 29, 2002
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From the Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
Received for publication, November 16, 2001, and in revised form, December 26, 2001
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ABSTRACT |
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Cyclic AMP receptor protein (CRP) is a
homodimeric protein, which is activated by cAMP binding to function as
a transcriptional regulator of many genes in prokaryotes. Until now,
the actual number of cAMP molecules that can be bound by CRP in
solution has been ambiguous. In this work, we performed a nuclear
magnetic resonance study on CRP to investigate the stoichiometry of
cyclic nucleotide binding to CRP. A series of
1H-15N heteronuclear single quantum
coherence (HSQC) spectra of the protein in the absence and in the
presence of cAMP or cGMP were analyzed. The addition of cAMP to CRP
induced a biphasic spectral change up to 4 equivalents, whereas the
cGMP addition made a monophasic change up to 2 equivalents. Altogether,
the results not only established for the first time that CRP possesses
two cyclic AMP-binding sites in each monomer, even in a solution
without DNA, but also suggest that the syn-cAMP binding
sites of the CRP dimer can be formed by an allosteric conformational
change of the protein upon the binding of two anti-cAMPs at
the N-terminal domain. In addition, a residue-specific inspection of
the spectral changes provides some new structural information about the
cAMP-induced allosteric activation of CRP.
Cyclic AMP receptor protein (abbreviated as
CRP1; also referred to as
catabolite gene activator protein, CAP) plays a key role in the
regulation of more than 150 genes in prokaryotes (1-4). CRP is
inactive in its apo form, i.e. in the absence of cAMP, but
it is activated by cAMP binding and functions by binding to specific
DNA sites, as well as by interacting with RNA polymerase. The protein
is a dimer composed of two identical subunits, each 209 amino acids
long. Several three-dimensional structures of the CRP·cAMP
complex, with or without DNA, have been solved by x-ray crystallography
(4-7). In these structures, each subunit of CRP is folded into two
structurally distinct domains, which are covalently connected by a
short polypeptide stretch named the hinge region (residues 135-138).
The larger N-terminal domain, which is predominantly At present, another matter of primary concern and interest regarding
CRP is the number of conformational states the protein can adopt with
cAMP and which one of the states is the active conformation. The many
biochemical and biophysical properties of CRP that exhibit a bimodal
dependence on cAMP concentration have been interpreted as evidence for
the existence of three conformational states of the protein (18-20).
During the 3 decades since its discovery, the protein has been thought
to be able to bind two cAMP molecules, and thus three conformational
states of CRP have been considered, namely apo-CRP,
CRP-cAMP1, and CRP-cAMP2 (18, 19). This
assumption has been supported by the crystal structures of the
CRP·cAMP2 and CRP·cAMP2·DNA complexes
(4-6), where two cAMP molecules are bound with an
anti-conformation in the N-terminal domains of the protein.
In addition, the second state, CRP·cAMP1, has been
considered to be the only active conformation of CRP (18, 19).
Recently, Passner and Steitz (4) solved the crystal structure of the CRP·cAMP4·DNA complex, where two additional cAMP
molecules with a syn-conformation are bound to the region
between the interdomain hinge and the C-terminal domain of the protein.
Thus, they reinterpreted the three conformers as represented by
apo-CRP, CRP·cAMP2, and CRP·cAMP4.
Afterward, several reports adopting this new model have appeared in the
literature (20, 21). However, this new paradigm for CRP is doubtful for
the following reasons, as pointed out by Harman (2). First, the new
model could not explain the fact that CRP is functionally activated
with one equivalent of cAMP (22-25). Second, aside from the existence
of a CRP·cAMP4·DNA crystal structure, there has been no
compelling experimental evidence for CRP·cAMP4 in
solution. In addition, the protein footprinting results of CRP showed
that the DNA binding of CRP probably alters the conformation of the
protein (26), and the DNA molecule also contributes to the
syn-cAMP binding in the crystal structure of CRP·cAMP4·DNA. Thus, it is not clear, in solution,
whether a CRP dimer in nature can bind four cAMP molecules or
CRP·cAMP2 can bind the additional two syn-cAMP
molecules only after binding DNA.
In the present work, we concisely analyzed the stoichiometry of the
cAMP binding to CRP in solution and in the absence of DNA, by NMR
spectroscopy. The results clearly revealed that CRP binds four cAMP
molecules as its maximum, even in the solution without DNA. In
addition, the comparative study of cGMP, an antagonist of cAMP
(13-15), provides new information about the allosteric conformational
change of CRP by cAMP binding.
99.9% D2O, cAMP, and cGMP were purchased from
Sigma, and all other materials were either analytical or
biotechnological grade. Uniformly 15N-labeled CRP was
prepared as reported previously (9). The absence of cAMP in the
purified CRP solution was checked dually by the absorbance ratio at 278 and 260 nm and by the near-UV circular dichroism spectrum shape of the
protein (9, 27-30). The concentrations of the protein and cyclic
nucleotides were determined spectrophotometrically using the following
extinction coefficients: 41,000 M As shown in Fig. 1, most of the
resonances in the HSQC spectra of CRP were perturbed upon the addition
of cAMP. This spectral change was completed with 4 molar equivalents of
cAMP for CRP (Fig. 1C) and showed a biphasic pattern with a
phase from 0 to 2 equivalents and the other from 2 to 4 equivalents of
cAMP. For example, as shown in Fig. 2,
the resonances Glu72 and Gly74 were
broadened by the addition of the first equivalent of cAMP and
subsequently disappeared with 2 equivalents of cAMP binding. Concomitantly, the peaks a and d, which seem to correspond to the
resonances of Glu72 and Gly74,
respectively, in the presence of cAMP, appeared through the binding of
the first two cAMPs, and no significant chemical shift change in these
resonances occurred with the further addition of cAMP. In contrast, the
chemical shift changes from the resonances Asp161,
Gly173, and Gly184, probably to the
respectively corresponding peaks b, e, and f, began when the molar
ratio of CRP to cAMP was 1:3 and were completed at the molar ratio of
1:4. Fig. 3 also clearly depicts the
biphasic spectral change of CRP upon cAMP binding. The resonance
Ile203 shifted, probably to peak a, with a
remarkable broadening through the binding of the first two equivalents
of cAMP, and then shifted again through the binding of the second two
equivalents of cAMP, probably to peak b. Fig.
4 also semiquantitatively shows the
spectral change of CRP by the binding of cAMP. Since the
sequence-specific NMR assignments of the cAMP-bound CRP were
impossible, we could not plot the chemical shift differences between
the apo- and cAMP-bound CRP forms. Instead, we analyzed the remaining
intensities of individual resonances. For several representative
resonances, the square root values of the relative intensity,
I/I0, are plotted in Fig. 4 as a
function of the molar equivalents of cAMP to CRP, where I
and I0 are the resonance intensities in the
presence or absence of cAMP, respectively. The
(I/I0)1/2 values are
representative of the unchanged or remaining fraction, based on the
fact that the resonance intensity is approximately proportional in
general to the square of the concentration, and its zero value
indicates that the resonance was completely broadened or shifted
elsewhere. Some cAMP-dependent intensity decreases were
completed (i.e. the peaks disappeared) when the molar ratio of CRP to cAMP was 1-2, while the others continued up to the ratio of
1-4. Only a few resonances from the N-terminal residues retained both
their chemical shift and intensity, independently of the added cAMP
concentration (Fig. 4). Although almost all of the resonances, except
for those from ~10 N-terminal residues, were perturbed upon cAMP
addition, the individual ending points of change could be identified
qualitatively or semiquantitatively for only 76 resonances; the
changing group A, consisting of 46 resonances that were completely
broadened or shifted elsewhere by the binding of 2 cAMP equivalents to
CRP, and the changing group B, consisting of 30 resonances whose
spectral changes were completed with 4 equivalents of cAMP. Their
corresponding residues are respectively summarized in Fig.
5. It is very likely that some of the
resonances of the former changing group were affected subsequently by
the second two equivalents of cAMP binding, as depicted for resonance
Ile203 (Fig. 3). Unfortunately, however, this could
rarely be identified for the changing group A resonances, due to the
lack of sequence-specific assignments in the [CRP]/2[cAMP] spectrum
(Fig. 1B). It was also likely that some resonances in group
B were changed by the first two equivalents of cAMP. For example, the
resonances Glu54 and Gly56, whose
intensity reductions were completed by 4 equivalents of cAMP, showed
more severe intensity decreases through the first 2 equivalents of cAMP
than the other resonances in group B (Fig. 4). Their chemical shifts
seemed to be slightly different in the [CRP]/2[cAMP] spectrum from
those in the apo-CRP spectrum (data not shown), but these chemical
shift changes were so small, with the concomitant broadening and
overlap, that they could not be confirmed.
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INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
-stranded, is
responsible for CRP dimerization, while the smaller C-terminal domain,
which is predominantly
-helical, is involved in specific recognition
of DNA. Although many biochemical and biophysical studies have implied
that cAMP binding allosterically induces CRP to assume an active
conformation (8-17), this allostery of CRP activation is not clearly
understood at the structural level, since the three-dimensional
structure of apo-CRP has not been solved yet.
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EXPERIMENTAL PROCEDURES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
1
cm
1 at 278 nm for the CRP dimer (8, 9); 14,650 M
1 cm
1 at 258 nm for cAMP (30);
12,950 M
1 cm
1 at 254 nm for
cGMP (30). The conventional two-dimensional
1H-15N HSQC spectra of 50 µM [U-15N]CRP dissolved in 50 mM potassium phosphate buffer (pH 6.0) containing 0.5 M potassium chloride, 7% D2O, and diverse
concentrations of cAMP or cGMP were obtained at 313 K on a Bruker DRX
600 spectrometer. All of the spectra were processed and analyzed using
the NMRPipe/NMRDraw software (31) and the NMRView program (32).
Residue-specific assignments were based on the previous report for
apo-CRP (8). Peak intensities were calibrated between spectra by making
the Gln6 resonance intensity of each spectrum equal
to each other, since the resonance retained the most constant chemical
shift and resonance intensity independently of the addition of cyclic nucleotides.
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RESULTS
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

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Fig. 1.
The two-dimensional
1H-15N HSQC spectra of 50 µM of CRP dimer in the presence of
cyclic nucleotides. The molar ratios of
[CRP]/[cAMP]/[cGMP] were 1/0/0 (A), 1/2/0
(B), 1/4/0 (C; red), 1/6/0
(C; black), 1/0/2 (D; red),
and 1/0/4 (D; black), respectively. The
blue-boxed regions were enlarged in Fig. 2.

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Fig. 2.
Selected strips taken from the
two-dimensional 1H-15N HSQC spectra of 50 µM of CRP dimer in the presence of
cyclic nucleotides. The molar ratios of
[CRP]/[cAMP]/[cGMP] were 1/1/0 (A), 1/2/0
(B), 1/3/0 (C), 1/4/0 (D;
black), 1/0/1 (E), 1/0/2 (F), and
1/0/0 (D; red), respectively.
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Fig. 3.
Spectral change of the Ile203
resonance upon cAMP binding. Two-dimensional
1H-15N HSQC spectra of 50 µM of
CRP dimer were obtained in the presence of 0 (A), 1 (B), 2 (C), 3 (D), and 4 (E) molar equivalents of cAMP, respectively. The peaks
"a" and "b" in the presence of cAMP are
the shifted resonances from Ile203 in apo-CRP.

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[in a new window]
Fig. 4.
Intensity changes upon cAMP binding.
Representative resonances with intensities that changed as a function
of cAMP concentrations were analyzed. The relative remaining fractions
are represented as the square root values of the intensity ratio,
I/I0; I and
I0 are the resonance intensities in the presence
and absence of cAMP, respectively.

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Fig. 5.
Mapping of the residues with resonances
affected by cAMP binding. The crystal structure of a CRP
subunit (ribbon presentation) with two bound cAMP molecules
(green) is illustrated, using the atomic coordinates
(accession number 2CGP in the Brookhaven Protein Data Bank) for a
subunit of CRP in the CRP·cAMP4·DNA complex (4). The
viewpoint is different between A and B, by the
relative rotation of the protein by about 180° with the long axis of
the C helix. Upon cAMP binding, the resonances from the red
residues first changed remarkably in the two-dimensional
1H-15N HSQC spectra of CRP, and subsequently
those from the blue residues changed. The suggested hydrogen
bonding patterns (9) in the C-terminal
-sheets (circled
region) are shown as dotted lines (C).
The spectral changes induced by the addition of cGMP were quite
different from those caused by cAMP. For instance, in Fig. 2, although
the resonances Glu72 and Gly74
disappeared, as observed with cAMP, through the 2 equivalents of cGMP
binding, the corresponding shift of the Glu72
resonance was gradually positioned probably to peak c instead of peak a
and that for Gly74 could not be observed. Moreover,
the further addition of cGMP above 2 equivalents caused no significant
change within the entire region in the HSQC spectra of CRP (Fig.
1D), indicating saturation at the molar ratio of 1:2 (CRP
dimer versus cGMP). All of the resonances changed by cGMP
binding were included in the changing group A, indicating that cGMP
seems to bind at a site in CRP similar to that occupied by the first 2 equivalents of cAMP. However, the identified chemical shift changes by
cGMP were not only different in their pattern, but were also smaller in
their degree than those caused by cAMP. This means that the
cGMP-induced conformational change of CRP, in contrast to that caused
by cAMP, is neither dramatic nor correct for activation.
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DISCUSSION |
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Despite the high molecular mass of the apo-CRP dimer (47 kDa), which has been considered rather large to be assigned by NMR, we previously obtained a nearly complete set of backbone NMR assignments of the protein, and determined the secondary structure of apo-CRP, by a series of multidimensional NMR spectra on the triply (13C, 15N, and 2H) labeled apo-CRP (8, 9). However, the low solubility, the low stability at high temperature (313 K), and the rapid relaxation time of the cyclic nucleotide-bound CRP prevented us from obtaining diverse three-dimensional NMR spectra, such as triple resonance spectra, which are essential for its sequence-specific NMR assignments (9). Instead, in this work, we obtained only the two-dimensional 1H-15N HSQC spectra of CRP in the presence of cyclic nucleotides, cAMP or cGMP, with rather good quality for the low concentration; higher concentrations (than 50 µM) reduced the spectral quality, due to precipitation during the measurements at 313 K. Both the impossibility of NMR assignments for the cyclic nucleotide-bound CRP and the severe spectral overlap in many regions of the HSQC spectra (Fig. 1) prevented us from achieving a complete and quantitative analysis of the individual resonances. Thus, the spectra were qualitatively or semiquantitatively analyzed, mainly in the well resolved region, on the basis of the previous backbone NMR assignments (8) of apo-CRP.
Despite some ambiguities, due to the insufficiency of the assignments for the cyclic nucleotide-bound CRP, the present results clearly revealed for the first time that a CRP dimer could bind four cAMP molecules in the absence of DNA in solution, forming two distinct cAMP-binding sites in each monomer. At least three stable conformational states of CRP with cAMP exist, namely apo-CRP, CRP·cAMP2, and CRP·cAMP4, as revealed by the present HSQC spectra in line with their crystal structures (3-6). In the presence of 1 or 3 equivalents of cAMP, the HSQC spectra of CRP became heterogeneous, with the doubling of many resonances. Unfortunately, it could not be determined whether the spectrum of CRP with 1 equivalent of cAMP reflects the intramolecular heterogeneity from a heterodimer with only one subunit that bound cAMP, or the intermolecular heterogeneity from the mixing of two distinct homodimeric proteins, apo-CRP and CRP·cAMP2. Likewise, the spectrum of CRP with 3 equivalents of cAMP could not prove by itself the conformational state of CRP·cAMP3. However, many functional aspects of CRP have been observed with only one equivalent of cAMP, and the crystal structure of a CRP mutant that bound three cAMP molecules has been solved (2, 22-25, 33). More experiments designed to distinguish the diverse conformational and functional states of CRP are necessary to understand the action mechanism of the protein, and we expect that the present results will provide important fundamental information for them.
The present study revealed that the maximum binding of cGMP, which is structurally quite similar to cAMP, is 2 equivalents for CRP. Cyclic GMP, compared with cAMP, made different and relatively small perturbations in the CRP spectrum; nevertheless, its binding site and affinity to CRP are relevant to those of the first 2 cAMP equivalents (9, 13-15). The different pattern and stoichiometry between cAMP and cGMP binding to CRP suggest the following hypothesis: the second two cAMP-binding sites in the CRP dimer are not innate and are formed by a conformational change of the protein upon the binding of the first two cAMP molecules at the two innate cyclic nucleotide-binding sites. The biphasic ordering of the cAMP-induced spectral change of CRP supports this assumption. This structural model can be depicted as a positive cooperativity between anti- and syn-cAMP binding. The severe broadening in the [CRP]/2[cAMP] spectrum (Fig. 1B), which was greater than that in any other CRP spectrum measured in this work, seems to support the positive cooperativity between the two distinct cAMP binding sites in CRP, under the conditions employed in this study. As a conclusion, the allosteric activation of CRP involves the conformational change by the cAMP binding in the N-terminal domain, and it probably leads to the formation of additional cAMP-binding sites near the C-terminal domain. In addition, it is apparent that the inactivity of CRP with cGMP is attributable to the absence of the correct allosteric conformational change of the protein.
A detailed inspection of the results provides additional information
about the cAMP-mediated conformational change of CRP. In the crystal
structure of CRP·cAMP4·DNA (3), two
anti-cAMP molecules are bound in the N-terminal domain, and
the other two syn-cAMP molecules are near the C-terminal
domain (Fig. 5). Consistently, in the present results, the residues
that were affected by the first 2 equivalents of cAMP binding to CRP
were mapped mainly in the N-terminal domain, including the interdomain
hinge and the helix D, while those affected by the second 2 equivalents were mainly in the C-terminal domain. There are two exceptional regions
in these maps. First, the region around residues Glu54 and
Gly56, despite its location in the N-terminal
domain, seems to be affected by the second 2 equivalents of cAMP
binding. This is since the region involves some residues that directly
interact with the syn-cAMP molecules in the crystal
structure of CRP·cAMP4·DNA (4). The second exception is
the C-terminal
-sheet, composed of
-strands 9, 10, 11, and 12, where at least 5 residues (Ile165, Leu195,
Ile203, Val205, and Gly207) were
reasonably affected by the first 2 equivalents of cAMP binding. This
was unexpected, since this
-sheet in the cAMP-bound CRP crystal is
located apart from the anti-cAMP binding sites, spatially as
well as in the sequence. Thus, it can be concluded that the C terminus
is closer to the N-terminal domain in apo-CRP than in cAMP-bound CRP. A
previous NMR study (9) showed that the C-terminal
-sheet is
conserved both in the apo- and cAMP-bound CRP, but its interstrand
hydrogen-bonding pattern in apo-CRP in solution slightly differed from
that of CRP·cAMP2 in the crystal (Fig. 4). For example,
apo-CRP in solution probably lacks the hydrogen-bonding between
Leu195 and Val205, which was observed in the
cAMP-bound CRP crystal. However, it is not clear whether these small
differences are really related to the conformational change or due to
the different conditions (solution versus crystal). The
present results clearly support the former proposal, in that the
resonances Ile165, Leu195, Ile203,
Val205, and Gly207 were obviously affected by
the binding of the first 2 equivalents of cAMP. In this
-sheet,
-strands 11 and 12 are important for DNA binding (34), and
-strands 9 and 10 are crucial for RNAP binding of CRP (35, 36).
Thus, the results indicate that the allosteric conformational change of
CRP, which is the functional activation process induced upon cAMP
binding, involves the spatial repositioning and the reconstitution of
the hydrogen-bonding pattern of the C-terminal
-sheet.
Although the structure of CRP bound to DNA has been solved, its
structure complexed with RNAP is not available. As a consequence, a lot
is known about the CRP·DNA contact, while in contrast, less is known
about the structural mechanism of the CRP-RNAP interaction. Cyclic AMP
mediates the protein-protein interaction between CRP and RNAP as well
as the CRP-DNA interaction, and the cAMP-bound CRP interacts with RNAP
in solution even in the absence of DNA (36, 37). As shown in the
present results, the cAMP-induced spectral perturbation of CRP was so
enormous that it necessarily involved the resonances from the residues
at or adjacent to the three RNAP-interacting regions (38) of the
protein. In addition, the binding of both the first (anti-)
and the second (syn-) cAMP affected those resonances (at
least His21, Glu54, Gly56,
Arg103, Asp155, Met157,
Thr158, His159, Asp161,
Gly162, Gln164, and Ile165, for
example). The C-terminal
-sheet of CRP, which seems to be readjusted
by the cAMP binding, also involves the major RNAP-binding sites
(residues Ala156-Gln164; Refs. 35 and 36).
Until now, no clear evidence that supports the cAMP-mediated
conformational change in the RNAP-interacting region of CRP has been
reported. Thus, the present results provide rather detailed structural
data for that conformational change and suggest that the
cAMP-dependent biphasic feature of the transcriptional regulation by CRP should be further studied at the structural level,
focusing on the CRP-RNAP interaction as well as the CRP-DNA interaction.
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ACKNOWLEDGEMENTS |
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We thank Prof. Yoshimasa Kyogoku and Prof. Hiroji Aiba for their generous gift of the CRP gene.
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FOOTNOTES |
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* This work was supported by a Korea Research Foundation Grant (KRF-2001-041-F00023) from the Ministry of Education, Korea, and in part by the 2001 BK21 project for Medicine, Dentistry and Pharmacy.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. Tel.: 82-2-880-7869;
Fax: 82-2-872-3632; E-mail: lbj@nmr.snu.ac.kr.
Published, JBC Papers in Press, January 7, 2002, DOI 10.1074/jbc.M112411200
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ABBREVIATIONS |
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The abbreviations used are: CRP, cyclic AMP receptor protein; HSQC, heteronuclear single quantum coherence; RNAP, RNA polymerase.
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