5
THE JOURNAL OF BIOLOGICAL CHEMISTRY 0 1989 by The American Soclety for Biochemistry and Molecular Bioloa, Inc Vol. 264, No. 34, Issue of December 5, pp. 20817-20821,1989 Printed m U.S.A. The Calcium-binding Site in the Galactose Chemoreceptor Protein CRYSTALLOGRAPHIC AND METAL-BINDING STUDIES* (Received for publication, February 21, 1989) Meenakshi N. Vyas, Bruce L. Jacobson, and Florante A. Quiocho From the Howard Hughes Medical Institute and Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030 and the Department of Biochemistry, Rice Uniuersity, Houston, Texas 77251 We have determined the relative affinities in solution for various metals which bind to the lone calcium- binding site of the D-galactose-binding protein which resembles the EF-hand loop. In order of affinity the metals are: Ca2+ z Tb3+ = Pb2+ > Cd2’ > Sr2+ > Mg2+ >> Ba2+. The binding affinity for calcium (Kd = 2 MM) and the slow off-rate determined for terbium (1 X s-l) and that the metal-binding site is unperturbedby sugar binding argue for a structural role. Furthermore, we have crystallographically refined the structure of the binding protein with the calcium substituted by cad- mium, compared it with the calcium-bound structure, and found them to be identical. The results of these structural and solution studies support the hypothesis that for a given metal-binding loop, cation hydration energy, size, and charge are major factors contributing to binding affinity. Calcium-binding proteins have received considerable atten- tion due to their diverse roles in biological systems. The vast majority of these sites conform to the EF-hand motif proposed by Kretsinger (Kretsinger and Nockolds, 1973), yet their affinities and specificities vary considerably(Levine and Wil- liams, 1982). Understanding the physical properties of cal- cium-binding loops has been difficult because in most proteins containing EF-hand type sites, the loops are paired (Kretsin- ger, 1987). The recent discovery (Vyas et al., 1987) of an EF- hand like calcium-binding site in the D-galactose-binding protein (GBP)’ (Mr - 32,000) provides further opportunity for eluci4ation of fundamental aspects of calcium binding. The 1.9-A highly refined structure (Vyas et al., 1988) of a protein with a lone high affinity calcium-binding site, free from cooperative effects often seen in other systems, allows direct correlation of the basic biochemical properties of affin- ity and specificity with structural properties. The structure of the GBP calcium-binding site has been described in detail elsewhere (Vyas et al., 1987) and will only be summarized here. The Ca2+ is bound in a 9-residue loop (residues 134-142) in the C-terminal domain. This loop, flanked by a reverse-turn and a @-strand, provides five oxygen ligands from every second residue. Glu-205 provides the last 2 oxygen ligands. There are no water molecules directly co- * This work was supported by the Howard Hughes Medical Insti- tute and by National Institutes of Health Grant GM-21371 and Welch Foundation Grant Q-581. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “aduertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. The abbreviations used are: GBP, D-galactose-binding protein; Pipes, piperazine-N,N’-bis(2-ethanesulfonic acid); EGTA, [ethylene- bis(oxyethylenenitrilo)]tetraacetic acid. ordinated to the calcium. The net charge of the coordinating ligands is -3. The coordination around the calcium is nearly pentagonally bipyramidal and superimposable with the EF- hand lovp of parvalbumin with a root mean square difference of 0.60 A. There are other marked similarities in the calcium site of GBP and the EF-hand loop. The purpose of these studies was 4-fold to confirm the existence of the metal-binding site revealed by x-ray crystal- lography; to determine its stoichiometry, affinity, and speci- ficity; to correlatebiochemical properties with structure; and to investigate the effect of sugar binding on thegeometry of the metal-binding site. MATERIALS AND METHODS Chernicak-Metals of the highest possible purity, calcium (11) chloride (99.99% pure), terbium (111) chloride hexahydrate (99.999% pure), magnesium (11) chloride (99.995%pure), strontium (11) chloride (99.995% pure), cadmium (11) chloride (99.99% pure), lead (11) chlo- ride (99.999% pure), and barium (11) chloride (99.999% pure) were obtained from Aldrich and used without further purification. DEAE- cellulose was obtained from Whatman. P-GDG andthe Bio-Rad Protein Assay were obtained from Bio-Rad. 45CaC12 was purchased from Du Pont-New England Nuclear. Pipes and Sephadex G-25/50 were obtained from Sigma. Protein Purification-GBP was purified as previously described (Parsons and Hogg, 1974) from Escherichia coli B/r ara39, and LA5709 containing the plasmid pVB2-wt was kindly provided by Dr. M. Manson, Texas A & M University (Scholle et al., 1987). Metal Solutiorz-Concentrated stocks (100 mM for all metals with the exception of PbC1, which was 10 mM) were prepared in deionized, glass distilled water. Due to the hygroscopic character of many of the metals used, concentrations were confirmed by EDTA titration. Metal stock solutions were stored for up to 1 week in plastic bottles at 4 “C. Sugar- and Metal-free GBP-For titrimetric experiments and sugar-binding studies, calcium- and sugar-free GBP was used. Like many binding proteins, purified GBP contains bound ligand (Miller et al., 1980, 1983; Pflugrath and Quiocho, 1988; Sack et al., 1989). This finding lead to the development of a mild and efficient method for removing bound ligand (Miller et al., 1980, 1983). By including EGTA with the solution originally found to remove bound glucose (Miller et al., 1980), it was possible to simultaneously remove bound calcium and bound glucose without loss of sugar-binding activity. The procedure is as follows. GBP was treated with 3 M guanidine HCl, 5 mM EGTA, 5 mM EDTA in 50 mM Tris-HC1, pH 8.2. Guanidine HC1 was removed by dialysis against 5 mM EDTA, 50 mM Tris-HC1, pH 8.2, followed by dialysis against 5 mM EDTA, 10 mM Tris-HC1, pH 7.4. Prior to metal-binding studies, EDTA and Tris- HCI were removed by passage through a Sephadex G-25/50 column equilibrated with 20 mM Pipes, pH 7.0. It was later discovered that the Sephadex column (polyglucose) released enough glucose to re- saturate GBP.To alleviate this problem a P-GDG (acrylamide based) column was used to remove Tris and EDTA. Fluorescence Spectroscopy-Fluorescence spectroscopy was per- formed on a SLM-Aminco model 4800 spectrofluorometer. The tem- perature was maintained at 20 “C with a circulating water bath. An excitation wavelength of 290 nm yielded efficient energy transfer while shifting the second order light beyond the terbium emission maximum (545 nm). Interestingly, at a slit width of 4 nm or below 20817

The Calcium-binding Site in the Galactose Chemoreceptor ... · 2.6 FM for Tb3' binding and of 4.7 PM calcium binding. The binding affinities of other metals in solution were determined

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Page 1: The Calcium-binding Site in the Galactose Chemoreceptor ... · 2.6 FM for Tb3' binding and of 4.7 PM calcium binding. The binding affinities of other metals in solution were determined

THE JOURNAL OF BIOLOGICAL CHEMISTRY 0 1989 by The American Soclety for Biochemistry and Molecular Bioloa, Inc

Vol. 264, No. 34, Issue of December 5, pp. 20817-20821,1989 Printed m U.S.A.

The Calcium-binding Site in the Galactose Chemoreceptor Protein CRYSTALLOGRAPHIC AND METAL-BINDING STUDIES*

(Received for publication, February 21, 1989)

Meenakshi N. Vyas, Bruce L. Jacobson, and Florante A. Quiocho From the Howard Hughes Medical Institute and Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030 and the Department of Biochemistry, Rice Uniuersity, Houston, Texas 77251

We have determined the relative affinities in solution for various metals which bind to the lone calcium- binding site of the D-galactose-binding protein which resembles the EF-hand loop. In order of affinity the metals are: Ca2+ z Tb3+ = Pb2+ > Cd2’ > Sr2+ > Mg2+ >> Ba2+. The binding affinity for calcium (Kd = 2 MM) and the slow off-rate determined for terbium (1 X s-l) and that the metal-binding site is unperturbed by sugar binding argue for a structural role. Furthermore, we have crystallographically refined the structure of the binding protein with the calcium substituted by cad- mium, compared it with the calcium-bound structure, and found them to be identical. The results of these structural and solution studies support the hypothesis that for a given metal-binding loop, cation hydration energy, size, and charge are major factors contributing to binding affinity.

Calcium-binding proteins have received considerable atten- tion due to their diverse roles in biological systems. The vast majority of these sites conform to the EF-hand motif proposed by Kretsinger (Kretsinger and Nockolds, 1973), yet their affinities and specificities vary considerably (Levine and Wil- liams, 1982). Understanding the physical properties of cal- cium-binding loops has been difficult because in most proteins containing EF-hand type sites, the loops are paired (Kretsin- ger, 1987). The recent discovery (Vyas et al., 1987) of an EF- hand like calcium-binding site in the D-galactose-binding protein (GBP)’ (Mr - 32,000) provides further opportunity for eluci4ation of fundamental aspects of calcium binding. The 1.9-A highly refined structure (Vyas et al., 1988) of a protein with a lone high affinity calcium-binding site, free from cooperative effects often seen in other systems, allows direct correlation of the basic biochemical properties of affin- ity and specificity with structural properties.

The structure of the GBP calcium-binding site has been described in detail elsewhere (Vyas et al., 1987) and will only be summarized here. The Ca2+ is bound in a 9-residue loop (residues 134-142) in the C-terminal domain. This loop, flanked by a reverse-turn and a @-strand, provides five oxygen ligands from every second residue. Glu-205 provides the last 2 oxygen ligands. There are no water molecules directly co-

* This work was supported by the Howard Hughes Medical Insti- tute and by National Institutes of Health Grant GM-21371 and Welch Foundation Grant Q-581. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “aduertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The abbreviations used are: GBP, D-galactose-binding protein; Pipes, piperazine-N,N’-bis(2-ethanesulfonic acid); EGTA, [ethylene- bis(oxyethylenenitrilo)]tetraacetic acid.

ordinated to the calcium. The net charge of the coordinating ligands is -3. The coordination around the calcium is nearly pentagonally bipyramidal and superimposable with the EF- hand lovp of parvalbumin with a root mean square difference of 0.60 A. There are other marked similarities in the calcium site of GBP and the EF-hand loop.

The purpose of these studies was 4-fold to confirm the existence of the metal-binding site revealed by x-ray crystal- lography; to determine its stoichiometry, affinity, and speci- ficity; to correlate biochemical properties with structure; and to investigate the effect of sugar binding on the geometry of the metal-binding site.

MATERIALS AND METHODS

Chernicak-Metals of the highest possible purity, calcium (11) chloride (99.99% pure), terbium (111) chloride hexahydrate (99.999% pure), magnesium (11) chloride (99.995% pure), strontium (11) chloride (99.995% pure), cadmium (11) chloride (99.99% pure), lead (11) chlo- ride (99.999% pure), and barium (11) chloride (99.999% pure) were obtained from Aldrich and used without further purification. DEAE- cellulose was obtained from Whatman. P-GDG and the Bio-Rad Protein Assay were obtained from Bio-Rad. 45CaC12 was purchased from Du Pont-New England Nuclear. Pipes and Sephadex G-25/50 were obtained from Sigma.

Protein Purification-GBP was purified as previously described (Parsons and Hogg, 1974) from Escherichia coli B/r ara39, and LA5709 containing the plasmid pVB2-wt was kindly provided by Dr. M. Manson, Texas A & M University (Scholle et al., 1987).

Metal Solutiorz-Concentrated stocks (100 mM for all metals with the exception of PbC1, which was 10 mM) were prepared in deionized, glass distilled water. Due to the hygroscopic character of many of the metals used, concentrations were confirmed by EDTA titration. Metal stock solutions were stored for up to 1 week in plastic bottles at 4 “C.

Sugar- and Metal-free GBP-For titrimetric experiments and sugar-binding studies, calcium- and sugar-free GBP was used. Like many binding proteins, purified GBP contains bound ligand (Miller et al., 1980, 1983; Pflugrath and Quiocho, 1988; Sack et al., 1989). This finding lead to the development of a mild and efficient method for removing bound ligand (Miller et al., 1980, 1983). By including EGTA with the solution originally found to remove bound glucose (Miller et al., 1980), it was possible to simultaneously remove bound calcium and bound glucose without loss of sugar-binding activity. The procedure is as follows. GBP was treated with 3 M guanidine HCl, 5 mM EGTA, 5 mM EDTA in 50 mM Tris-HC1, pH 8.2. Guanidine HC1 was removed by dialysis against 5 mM EDTA, 50 mM Tris-HC1, pH 8.2, followed by dialysis against 5 mM EDTA, 10 mM Tris-HC1, pH 7.4. Prior to metal-binding studies, EDTA and Tris- HCI were removed by passage through a Sephadex G-25/50 column equilibrated with 20 mM Pipes, pH 7.0. It was later discovered that the Sephadex column (polyglucose) released enough glucose to re- saturate GBP. To alleviate this problem a P-GDG (acrylamide based) column was used to remove Tris and EDTA.

Fluorescence Spectroscopy-Fluorescence spectroscopy was per- formed on a SLM-Aminco model 4800 spectrofluorometer. The tem- perature was maintained at 20 “C with a circulating water bath. An excitation wavelength of 290 nm yielded efficient energy transfer while shifting the second order light beyond the terbium emission maximum (545 nm). Interestingly, at a slit width of 4 nm or below

20817

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20818 Metal-binding Site in Galactose-binding Protein

the terbium emission peak split into two peaks located a t 542 and 548 nm.

Tb"' additions not exceeding 15 pl total were made with a Hamilton syringe to a starting volume of 3 ml of calcium- and sugar-free protein ([GBP] = 5 pM). Spectra were taken from 530 to 570 nm with a slit width of 4 nm. To minimize noise, 10 measurements were taken a t each wavelength and averaged internally by the instrument. The extent of Tb3+ binding was determined by calculating the area under the major Tb"' emission peak (546-554 nm) using the software supplied with the instrument.

Crystallographic Refinement of Structure-Metal replacement was accomplished by soaking native GBP crystals in 10 mM sodium citrate, pH 5.1, containing 2 mM cadmium for 1 week. The cadmium data was originally used in the MIR analysis (Vyas et al., 1983). The methods normally used in our laboratory for measuring and process- ing intensity data are described elsewhere (Pflugrath and Quiocho, 1988; Sack et al., 1989).

The same strategy used in the refinement of the structure of native GBP was adapted in the refinement of the structure of GBP with the calcium replaced by cadmium. The PROLSQ restrained least-squares refinement program was used in the refinement (Hendrickson, 1985), and refined models superimposed on electron density maps were examined with PSFRODO (Pflugrath et al., 1984; version 6.6 by J. S. Sack in our laboratory) running on PS350 or PS390.

RESULTS AND DISCUSSION

Terbium has been used extensively to investigate calcium- binding sites (Gross et al., 1987; Horrocks and Collier, 1981; Horrocks and Sudnick, 1981; Luk, 1971; Nelson et al., 1977). This popularity is due to several characteristics of terbium which not only render it useful in determining binding stoi- chiometry, but make it sensitive to the nature of the binding site as well. Proteins with high-affinity calcium-binding sites bind terbium stoichiometrically and specifically without sig- nificant structural changes (Horrocks, 1982). Additionally, protein-bound terbium experiences considerable enhance- ment of its characteristic green fluorescence due to Forster dipole-dipole energy transfer from aromatic residues near the binding site (Horrocks and Sudnick, 1981). The intensity of the terbium fluorescence is dependent on the efficiency of this energy transfer which is in turn dependent on the distance from the donor (tryptophan) to the acceptor (terbium), the geometry of the tryptophan and the terbium, the overlap integral for tryptophan fluorescence and terbium absorbance, and the refractive index of the medium (Cantor and Schim- mel, 1980).

There are many instances in which the metal bound in proteins could be displaced stoichiometrically by terbium titration (Luk, 1971; Gross et al., 1987). This was not the case with GBP; attempts to titrate native GBP with terbium yielded no change in terbium fluorescence. However, if GBP was incubated with 20-fold excess terbium, displacement of calcium with an accompanying increase in terbium fluores- cence was observed over time, suggesting that a slow calcium off-rate was the cause of this difficulty. Indeed, calcium- and sugar-free GBP (see "Materials and Methods") could be ti- trated with Tb3+ to an end point of l mol of Tb3' added per mol of GBP. Additionally, the off-rate for terbium, estimated from the observed rate of terbium displacement by a 1000- fold excess of calcium, is 3 X s-'. The predicted on-rate for terbium based on the above off-rate and the Kd below is 1.2 x lo3 M-' s-'. The off-rate for calcium could not be determined directly because high concentrations of terbium can cause protein aggregation (Gross et al., 1987). Scatchard plots (Fig. 1) of the results of the terbium titration and the calcium equilibrium dialysis experiment indicate Kd values of 2.6 FM for Tb3' binding and of 4.7 PM for calcium binding.

The binding affinities of other metals in solution were determined by their ability to displace bound terbium, similar to the method described by Luk (1971), or their ability to

0.3

0.2

0.1

0.0 4 0.0 0.2 0.4 0.6 0.8 1 .0 1 .2

Y FIG. 1. Scatchard plot of calcium (X) and terbium (W) bind-

ing to GBP. Calcium data were obtained by equilibrium dialysis, whereas terbium data are from a fluorescene titration of metal-free protein. Solid lines indicate least squares fits of the data which yield Kd values of 4.7 p M for calcium and 2.6 p M for terbium.

TABLE I Properties of metals which bind to GBP

Dissociation constants (Kd) were determined by competition with calcium or terbium as described in the text, using independently determined values for calcium (4.7 pM) and terbium (2.6 p M ) . Values in parentheses indicate standard deviations.

Metal K d

Dialysis Fluorescence ACsd" Ionic radiusb

CcM kcallmol A M e 190 (20) 460 (30) -439 0.66 Tb3+ 5 (1) -815 0.92 Cd2+ 60 (20) 60 (5) -415 0.97 Ca2+ 2.0 (0.2) -362 0.99 Sr2+ 130 (30) 110 (5) -345 1.12 Pb2+ 5 (1) -343 1.20 Ba2+ 2000 (200) -331 1.34

a Marcus, 1985. Weast, 1987.

compete with 45Ca2f in an equilibrium dialysis experiment similar to the method described by Newcomer et al. (1979). The dissociation constants, size, and hydration energy for each cation used in this study are summarized in Table I.

Previously attempts have been made to correlate binding affinity with differences in cation size (Chao et al., 1984). Our experiments were designed to test the cation size hypothesis for a single, independent binding site. We found that the size criteria alone is unable to predict the relative affinities of the metal cations used in this study because it ignores the fun- damental importance of hydration energy in coordination chemistry as stressed by Cotton and Wilkinson (1988), "The process of forming [complexes] in aqueous solution. . . is really one of displacing one set of ligands, which happen to be water molecules, with another set." When solvation is considered, the binding energy of the protein-cation complex can be rigorously described as:

AG = AGss + AGpp + AGLL + AGps + A G u + AGPL + A G P L ~ (1)

where S represents a molecule of the solvent, P is a protein molecule, and L is a ligand molecule. In dilute solution, the contributions of the LL and PP interactions are negligible.

Page 3: The Calcium-binding Site in the Galactose Chemoreceptor ... · 2.6 FM for Tb3' binding and of 4.7 PM calcium binding. The binding affinities of other metals in solution were determined

Metal-binding Site in Galactose-binding Protein

Furthermore, GBP is fundamentally different from many other calcium binding loops (e.g. calmodulin) in that it does not undergo a significant conformational change upon cation binding (see below), thus the SS interactions, which represent the hydrophobic effect, remain essentially constant. Thus, Equation 1 simplifies to:

AG = AGps + A G u + AGPL + A G p s (2)

AGps is a property of the protein and constant for a given set of experimental conditions, and similarly, AG,, the cation hydration energy, is characteristic for a given cation. The crystal structures of Ca2+ and Cd2+ bound to GBP show that no water is directly coordinated to the cation. Furthermore, the location of crystallographically determined water mole- cules near the metal-binding site to be identical in both structures indicating that at least for the cadmium case, AGpm does not vary greatly with the nature of the metal bound. Note these are ordered, bound, water molecules near the site; there are no waters directly involved in cation binding. Thus, differences between the relative cation-binding affinities pre- dicted by hydration energy alone and the experimentally determined order reflect the contributions of the AGPL term.

Below are three series of relative binding affinities: that predicted by hydration energy alone, that predicted by size relative to calcium, and the experimentally determined order. It is quite clear that neither hydration energy alone nor sue alone can account for the experimental data. However, if the experimental results are compared carefully with the predic- tions some very useful information about the metal-binding site of GBP emerges.

Predicted

Hydration energy: Ba2+ > Pb2+ > Sf+ > CaZ+ > Cd2+ > M e > Tb3+

Cation size: Ca2+ > Cd2+ > Tb3+ > SrZ+ > Pb2+ > M$+ > Ba2+

Experimental: T b 3 + = Ca2+ = Pb2+ > Cdz+ > Sf+ > Mg'+ > Ba2+

The most striking difference between the relative affinities

FIG. 2. Stereo view of the metal- binding loop and the two flanking tryptophans from the refined struc- ture of Ca-GBP (blue) superimposed on the refined Cd-GBP structure (magenta). The electron density maps of both structures were calculated with ( I F, I - I F, I, a,) residual map in which the contribution of the metal in each struc- ture was omitted in the structure factor calculation. The density was contoured at 2 u of the difference map. No other density peak was observed in the entire asymmetric unit. The bound metals are 5.8 A from the center of the siq-mem- bered ring of Trp-127 and 11.4 A from the center of the six-membered ring of Trp-133. Note that the tryptophans are in the herringbone arrangement and the two refined structures overlap almost perfectly. See Table I1 for the final re- finement statistics of both structures.

20819

predicted by hydration energy alone and the experimental results is that barium and terbium are interchanged. Barium is the least strongly hydrated of the metals studied, and therefore predicted to bind tightly to the calcium-binding site. The best explanation for its low binding affinity is that its large unhydrated ionit radius (ri = 1.34 A) and the Ba-0 bond length of 2.76 A observed in small molecule crystal structures (Lonsdale et al., 1985) are beyond the size limit of the binding site irrespective of any advantage provided by its low hydration energy. This size limit is more clearly defined by Pb2+ and SF2+ which compete efficiently for the binding site in spite of their relative size. Thus, there appears to be a critical cationic radii between 1.20 (Pb") and 1.34 A (Baz') above which binding affinity decreases significantly, presum- ably due to steric constraints. Below this limit, cation hydra- tion energy is an important factor in determining binding affinity.

Hydration energy alone also fails to properly predict the tight binding affinity of terbium. This is because hydration energy, which describes the stability of a metal-water complex, reflects the greater stability imparted to a complex when the charge of the central metal is increased. The stronger inter- actions of terbium with its ligands no doubt also occur in the protein, leaving size as the principal determining factor in terbium binding affinity to the GBP site. It should be noted that the net charge of the metal-free GBP site is -3, adequate to stabilize the added charge of terbium.

Differences in calcium- and cadmium-binding affinities have been attributed to cadmium's preference for 6-fold co- ordination (Szebenyi and Moffat, 1986). To further probe this possibility, we have studied cadmium binding to GBP in solution (Table I) and in crystals (Table 11). Fig. 2 shows a ball and stick drawing of the calcium-binding site and the superimposed electron density of bound calcium and bound cadmium. Ca-0 and Cd-0 distances from the refined struc- tures are compared in Fig. 3. Coordination of the two metals, and positions of surrounding protein residues are identical

Page 4: The Calcium-binding Site in the Galactose Chemoreceptor ... · 2.6 FM for Tb3' binding and of 4.7 PM calcium binding. The binding affinities of other metals in solution were determined

20820 Metal-binding Site in Galactose-binding Protein

+Z

a,bU ' /

ASP (2.2

-Y

\ Am136

(2.59,2.58)

1.29) 061

FIG. 3. The coordinating ligands (all protein oxygen atoms) to metal (Ca2+ or Cd") bound to GBP superimposedoon an octahedron corresponding to a ligand distance of 2.41 A. Note that in reality the metal coordination is a distorted pentagonal bipyramid with the pentagon in the plane of the figure. The protein atoms are identified together with the octahedral designations. The numbers in parentheses indicate experimental Ca-0 distance fol- lowed by Cd-0 distance (in A). The Cd-0 bond lengths are con- sistent with those observed in small molecule structures of seven- coordinate cadmium complexes (Cameron et al., 1972; Harrison and Trotter, 1972).

within the error of the experiment. This is consistent with NMR experiments of other proteins which predict identical environments for bound calcium and cadmium (Cavi! et al., 1979; Vogel et al., 1985). The lower stability of the Cd2+. GBP complex in solution, can be attributed, in part, to hydration energy. However, the difference between calcium's and cad- mium's hydration energies is much greater than the difference in their binding energy implying that other factors stabilize, rather than destabilize the GBP. Cd2+ complex. In light of the close structural similarities of the two complexes, and the above discussion of the calcium- and cadmium-binding affin- ities to GBP in solution, it is unlikely that cadmium's pref- erence for 6-fold coordination is responsible for its lower binding affinity.

Previous investigations of other systems (Chao et al., 1984) have attributed the low binding affinity of magnesium solely to its small size relative to calcium. However, if the GBP site discriminated against cations smaller than calcium in the same manner as it does against those that are larger, then magnesium, because of its small size and high hydration energy, would be expected to be the worst competitor for the binding site. The data do not support this prediction. Rather, magnesium competes well with calcium and terbium. Thus, it seems that the small size of magnesium contributes positively to complex stability offsetting the adverse effect of its high hydration energy. This is consistent with the observed relative affinities of Group IIA elements in their complexes with hydroxycarboxyic acids, polycarboxylic acids, and polyami- nocarboxylic acids: Mg < Ca > Sr > Ba (Cotton and Wilkin- son, 1988).

One of the advantages of using terbium as a calcium probe is its sensitivity to environment. The dependence of transfer efficiency on the distance between the donor tryptophan residue and terbium to the sixth power makes it particularly responsive to small conformational changes about the cal- cium-binding site. The excitation spectrum of GBP com- plexed with Tb3+ exhibits a peak at 291 nm indicating that a tryptophan residue is primarily responsible for the energy

TABLE I1 Summary of restrained parameter refinement of the Ca-GBP and

Cd-GBP structures The values enclosed in parentheses are the target u associated with

each parameter, and are the inverse square root of the least squares weights of the corresponding restraints. The final values given are the root mean square deviations of the parameters from their respec- tive ideal values from the standard nroum listed.

u 1

Ca-GBP Cd-GBPb

R-factor 0.134 0.139 Resolution range (A) 10-2.5 10-2.5 Total reflections used 9258 9254 Overall B-value (A2) 18.04 19.30 Root mean square coordinate 0.010 0.012

Root mean square B-shift (A') 0.28 0.34 Average ( I Fo I - I Fc I 1 31.67 (14, -70) 29.54 (12, -70) Bond distances (A) 0.017 (0.015) 0.015 (0.015) Angle distances (A) 0.043 (0.025) 0.041 (0.025) Planarity (A) 0.009 (0.010) 0.008 (0.010) Chiral volume ( A 3 ) 0.064 (0.050) 0.062 (0.050) Angle w (") 6.3 (3.0) 6.2 (3.0) No of atoms refined

shift ( A )

Protein 2348 2348 D-Glucose 12 12 Metal Ca2+ Cd'+ Water oxygens 214 214 ' Although the original native structure of GBP was refined at 1.9-

A resolution (Vyas et al., 1987), it was re-refined at 2.5-A resolution in the present study for direct comparison with the Cd-GBP structure.

*The parameters for cadmium incorporated in PROFFT were kindly provided by Dr. Barry Finzel, Upjohn Co. The refined 1.9-A native structure was used as starting protein model in the refinement of Cd-GBP. Six crystals were used to collect diffraction intensities. The overall R-merge is 0.058. For all the individual crystal data sets; R-sym varied from 0.029 to 0.065 and R-overlap, which measures the agreement of a single crystal data set to the final merged data set, varied from 0.05 to 0.072.

transfer. The bound cation is 5.8 A fr9m the center of the six- membered ring of Trp-127 and 11.4 A from the center of the six-membered ring of Trp-133. We believe that Trp-127 is primarily responsible for energy transfer to bound terbium because of its proximity to the binding site (see Fig. 2). Contribution from Trp-133 is possible, but presumably minor because of the relative weakness of energy transfer fro? tryptophan to terbium exemplified by the Ro value of 3.35 A obtained by Horrocks and Sudnick (1981) for the parvalbumin system.

We explored the possibility that sugar binding could affect the environment of the bound terbium. Neither D-galaCtOSe nor D-glucose (also a substrate) binding to sugar-free, ter- bium-loaded GBP causes a change in terbium fluorescence (data not shown). The sugar-binding site is approximately 30 A from the calcium-binding site and the tryptophan nearest the bound calcium (Vyas et al., 1987). Thus, the lack of change in terbium fluorescence upon sugar binding indicates identical local geometry of the calcium-binding site in the presence and absence of sugar. Similarly, the intrinsic protein fluorescence spectra of calcium-free and calcium-bound GBP were com- pared in the presence and absence of substrate to determine whether occupancy of the metal site affected sugar binding. No discernible differences were observed (data not shown).

The above results are consistent with the proposed sugar binding mechanism. Crystallographic studies of periplasmic binding proteins have established a structural theme which has been consistently maintained by each of the six structures solved so far (Sack et al., 1989); all are composed of two domains connected by a flexible hinge region, with the ligand bound in the cleft between the two domains. Previous studies

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Metal-binding Site in Galactose-binding Protein 2082 1

suggest that ligand binding occurs via a hinge-bending motion in which the two domains move somewhat like a "Pac-Man" about the hinge region between the domains (Newcomer et al., 1981a, 1981b; Sack et al., 1989). According to the Pac- Man model, the conformational change is confined to the flexible hinge region. The two domains move toward each other, but preserve their individual structure. The calcium- binding site, located at one end of the ellipsoidal protein, well away from the cleft and the sugar-binding site, would not be expected to experience a change in environment.

On the basis of affinity for calcium, EF-hands have been classified into two groups, structural and regulatory. Struc- tural sites (e.g. parvalbumin and the C-terminal domains of troponin C) have Kd values for calcium binding of -lo-' M, and Mg2+ is thought to compete for these sites under physio- logical conditions, whereas regulatory sites (e.g. calmodulin, N-terminal domains of troponin C, intestinal calcium-binding protein) have Kd values of M and are not believed to bind Mg2+ under physiological conditions (Satyshur et al., 1988; Levine and Williams, 1982).

Observations that cation dissociates very slowly (kOff = 3 x s-') for the GBP . Tb3+ complex and that substrate bind-

ing does not perturb terbium fluorescence support a structural role for the calcium-binding site of GBP. Additionally, of the EF-hand sites, site I or the CD-hand of parvalbumin (a structural site), most closely resembles the GBP site (Vyas et al., 1987). The CD hand and the GBP site differ from other calcium-binding loops at position 9 (Gln in GBP and Glu in the CD loop) which is of sufficient length for the side chain oxygen to coordinate directly to the calcium ion. In contrast, the side chain at this position in other EF-hand loops is too short, and a bound water molecule bridges the gap between the side chain and the calcium (Herzberg and James, 1985; Kretsinger, 1987). In spite of the close similarity with the CD- hand calcium-binding loop, calcium binding to the GBP site, which lacks flanking helices, is 2 orders of magnitude weaker.

This disparity in affinity values, which at first may appear inconsistent with a structural role, is actually a consequence of the different cellular locations of GBP and parvalbumin. The affinity of the CD loop for calcium (-IO-' M) and mag- nesium ( - l O w 3 ~ ) ensures that at physiological concentrations the site will be saturated with one of these metals (Levine and Williams, 1982). Presumably, free calcium concentrations in the periplasm are similar to extracellular concentrations observed for other systems M (Levine and Williams, 1982)). Therefore, GBP, despite its relatively low Kd, is certain to be saturated with calcium under physiological conditions. Furthermore, the GBP calcium-binding site and sugar-bind- ing site are functionally independent. In addition, regulatory sites, such as those found in calmodulin, release calcium rapidly (k,ff - 10 s-' (Fors6n et al., 1986)), enabling them to respond quickly to changes in calcium concentration. In con- trast to calmodulin, and consistent with a structural role, terbium is released slowly from the calcium site of GBP.

REFERENCES Cameron, A. F., Nuttall R. H., and Taylor, D. W. (1972) J . Chem.

SOC. Dalton Trans. 1608-1614

Cantor, C. R., and Schimmel, P. R. (1980) Biophys. Chem. 21,448- 451

Cavi., A., Daures, M.-F., Parello, J., Saint-Yves, A., and Sempere, R. (1979) Biochimie (Paris) 6 1 , 755-765

Chao, S., Suzuki, Y., Zysk, J. R., and Cheung, W.-Y. (1984) Mol. Phnrmacol. 26,75-82

Cotton, F. A., and Wilkinson, G. (1988) Advanced Inorganic Chem- istry, 5th Ed., John Wiley & Sons, New York

Forskn, S., Drakenberg, T., and Vogel, H. (1986) in Calcium and Cell Function (Cheung, W.-Y., ed) Vol. VI, pp. 113-157, Academic Press, Orlando, FL

Gross, M. D., Nelsestuen, G. L., and Kumar, R. (1987) J. Bid. Chem. 262,6539-6545

Harrison, W., and Trotter, J. (1972) J. Chem. SOC. Dalton Trans.

Horrocks, W. D., Jr. (1982) Adu. Znorg. Biochem. 4 , 201-261 Horrocks, W. D., Jr., and Collier, W. E. (1981) J. Am. Chem. SOC.

Horrocks, W. D., Jr., and Sudnick, D. R. (1981) Acct. Chem. Res. 14 ,

Hendrickson, W. A. (1985) Methods Enzymol. 115 , 252-270 Herzberg, O., and James, M. N. G. (1985) Biochemistry 2 4 , 5298-

Kretsinger, R. H., and Nockolds, C. E. (1973) J. Biol. Chem. 2 4 8 ,

Kretsinger, R. H. (1987) Cold Spring Harbor Symp. Quant. Biol. 5 2 ,

Levine, B. A., and Williams, R. J. P. (1982) in Calcium and Cell Function (Cheung, W.-Y., ed) Vol. 11, pp. 1-38, Academic Press, Orlando, FL

Lonsdale, K. (1985) International Tables for X-ray Crystallography, Vol. 111, pp. 257-274, Reidel Publishing Co., Dordrecht, Holland

Luk, C. K. (1971) Biochemistry 10, 2838-2843 Marcus, Y. (1985) Zon Solvation, John Wiley & Sons, New York Miller, D. M., 111, Olson, J . S., and Quiocho, F. A. (1980) J. Biol.

Miller, D. M., 111, Olson, J. S., Pflugrath, J. W., and Quiocho, F. A.

Nelson, D. J., Miller, T. L., and Martin, R. B. (1977) Bioinorg. Chem.

Newcomer, M. E., Miller, D. M., 111, and Quiocho, F. A. (1979) J. Biol. Chem. 254,7529-7533

Newcomer, M. E., Gilliland, G. L., and Quiocho, F. A. (1981a) J. Biol. Chem. 256,13213-13217

Newcomer, M. E., Lewis, B. A., and Quiocho, F. A. (1981b) J. Biol. Chem. 256,13218-13222

Parsons, R. G., and Hogg, R. W. (1974) J. Biol. Chem. 249 , 3602- 3607

Pflugrath, J. W., and Quiocho, F. A. (1988) J. Mol. Biol. 200 , 163- 180

Pflugrath, J . W., Saper, M. A., and Quiocho, F. A. (1984) in Compu-

407, Clarendon Press, Oxford tational Crystallography (Hall, S. R., and Ashida, T., eds) pp. 404-

Sack, J. S., Saper, M. A., and Quiocho, F. A. (1989) J. Mol. Biol. 206 ,

Satyashur, K. A., Rao, S. T., Pyzalska, D., Drendel, W., Greaser, M.,

Scholle, A., Vreemann, J., Blank, V., Nold, A,, Boos, W., and Manson,

Szebenyi, D. M. E., and Moffat, K. (1986) J. Biol. Chem. 261,8761-

956-960

103,2856-2862

384-392

5302

3313-3326

499-510

Chem. 255,2465-2471

(1983) J. Biol. Chem. 258 , 13665-13672

7, 325-334

171-191

and Sundarlingam, M. (1988) J. Biol. Chem. 263,1628-1647

M. (1987) Mol. Gen. Genet. 208 , 247-253

8777 Vogel, H. J., Drakenberg, T., Forshn, S., O'Neil, J. D. J., and Hof-

Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1987) Nature 327,

-. . .

mann, T. (1985) Biochemistry 24,3870-3876

635-638 Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1983) Proc. Natl. Acad.

Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1988) Science 242 ,

." ."

Sci. U. S. A. 80, 1792-1796

1290-1295 Weast, R. C. (1987) CRC Handbook of Chemistry and Physics, CRC

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Press Inc., Boca Raton, FL