Mutations at the intersubunit metal-binding site had no effect, whereas mutation at Glu139, which is part of the peripheral metal-binding site found in pyrophosphatase crystals near the c
Trang 1Cd2+-induced aggregation of Escherichia coli pyrophosphatase
Yury V Zimenkov1, Anu Salminen2, Irina S Efimova1, Reijo Lahti2and Alexander A Baykov1
1 A N Belozersky Institute of Physico-Chemical Biology and School of Chemistry, Moscow State University, Moscow, Russia;
2 Department of Biochemistry, University of Turku, Finland
We report here that Escherichia coli pyrophosphatase
aggregates in the presence of millimolar Cd2+ This highly
cooperative process was specific to both the metal ion and
the protein and could be reversed fully by decreasing the
Cd2+concentration Aggregation was enhanced by Mg2+,
the natural cofactor of pyrophosphatase, and Mn2+
Mutations at the intersubunit metal-binding site had no
effect, whereas mutation at Glu139, which is part of the
peripheral metal-binding site found in pyrophosphatase
crystals near the contact region between two enzyme mole-cules, suppressed aggregation These findings indicate that aggregation is affected by Cd2+binding to the peripheral metal-binding site, probably by strengthening intermole-cular Trp149–Trp149¢ stacking interactions
Keywords: aggregation; cadmium; inorganic pyrophospha-tase; site-directed mutagenesis
Protein aggregation is a common phenomenon, with
important practical implications A variety of diseases,
including the amyloidoses and prion diseases, as well as
other protein deposition disorders, involve protein
aggre-gation [1] In most cases, the proteins that aggregate are
totally or partially unfolded, and the aggregation, which
occurs via hydrophobic interactions, is almost completely
irreversible [2,3] Examples of proteins aggregating in their
native state, other than salting out and isoelectric point
precipitation, are less common, with the aggregation of the
mutant hemoglobin that causes sickle-cell anemia being
the best known example [4] In addition, Zn2+and other
divalent cations have been reported to aggregate native
dodecameric glutamine synthethase into tubular structures
[5] and to have a role in amyloid formation [6,7]
Escherichia coliinorganic pyrophosphatase (PPase) is an
essential enzyme that converts pyrophosphate, a byproduct
of many biosynthetic reactions, into phosphate [8] The
native PPase molecule is formed by six identical subunits, of
20 kDa each, arranged in parallel layers of trimers [9,10]
Each subunit has an active site, resembling a large cavity,
with subsites for two phosphate molecules and four divalent
metal ions that can act as cofactors (Mg2+, Mn2+) or
inhibitors (Ca2+) In the absence of pyrophosphate or
phosphate, only two Mg2+ions are bound to the active site
[11] In addition, one Mg2+ion is bound at the intertrimeric
interface, where it is octahedrally associated with six water molecules, which in turn hydrogen bond to the Asn24 and Asp26 residues of the two interacting subunits [12,13] PPase is a readily soluble enzyme that shows no tendency
to aggregate in a variety of conditions We show here, however, that this enzyme reversibly aggregates in the presence of Cd2+, a common polluting ion that is toxic to
E coliat millimolar concentrations [14], and we describe the mechanism behind this aggregation
Materials and methods
Wild-type E coli PPase and PPase variants were prepared and purified as described previously [15] The final prepa-rations were homogeneous, according to SDS/PAGE Enzyme aggregation was followed by measuring the absorbance of enzyme solution at 440 nm in a quartz cuvette
of 1 cm path length In kinetic experiments, an aliquot of 0.1M cadmium acetate solution was added to 0.7 mL of enzyme solution (0.37 mgÆmL)1) containing 0.1MTris/HCl (pH 7.2), 1 mMMgCl2and 5 mMdithiothreitol; the contents
of the cuvette were rapidly mixed and the absorbance was recorded on a Pharmacia-LKB Ultrospec Plus spectropho-tometer In titration experiments, metal salt was added in 1.4 lL increments, the contents of the cuvette were stirred for 3 min, and the absorbance of the solution was measured This time was selected on the basis of the observation that
3 min was sufficient for aggregation to reach > 85% of its equilibrium level under a variety of conditions Each titration was repeated at least three times, and the SD value for the parameter describing the titration curve (c½) was calculated Except where stated otherwise, aggregation of 0.37 mgÆmL)1solutions of PPase was measured at 20C
in a buffer at 0.1Mionic strength
The initial rates of PPihydrolysis were measured by a continuous Pi assay [16] in a reaction mixture containing
20 lMPPi, 20 mM MgCl2, 0.15M Tris/HCl (pH 7.2), and 0.2 mM EGTA The reaction was initiated by adding enzyme (4–10 ngÆmL)1final concentration) and was carried out for 3–4 min at 25C
Correspondence to R Lahti, Department of Biochemistry, University
of Turku, FIN-20014 Turku, Finland Fax: + 358 2333 6860,
Tel.: + 358 2333 6845, E-mail: reijo.lahti@utu.fi; or A A Baykov,
A N Belozersky Institute of Physico-Chemical Biology and School of
Chemistry, Moscow State University, Moscow 119899, Russia.
Fax: + 7095 9393181, Tel.: + 7095 9395541,
E-mail: baykov@genebee.msu.su
Abbreviations: c ½ , values for the parameter describing the titration
curve; PPase, Escherichia coli inorganic pyrophosphatase.
Enzyme: inorganic pyrophosphatase (EC 3.6.1.1).
(Received 23 March 2004, revised 26 May 2004, accepted 1 June 2004)
Eur J Biochem 271, 3064–3067 (2004) FEBS 2004 doi:10.1111/j.1432-1033.2004.04239.x
Trang 2Results and discussion
General characteristics of PPase aggregation
Upon addition of 2 mMCd2+, we noted the development of
turbidity in the PPase solution, with a gradual increase in
absorbance at 440 nm owing to light scattering by aggregate
particles (Fig 1) After sedimenting the aggregated protein
in an Eppendorf microcentrifuge, less than 10% of PPase, as
measured by activity and protein content, remained in the
supernatant The aggregated PPase could be easily
solubi-lized, with a complete recovery of activity, by suspending the
sediment in buffer containing no cadmium salt, indicating
that the native tertiary structure is regained when the Cd2+
is removed
The dependence of aggregation on Cd2+concentration
was characteristic of a highly cooperative process (Fig 2)
Virtually no aggregation was observed at concentrations of
< 1 mMCd2+, whereas, at 1.5 mMCd2+, the aggregation was nearly complete The theoretical curve, shown in Fig 2, was constructed assuming that the aggregation depends on the 12th(!) power of Cd2+concentration
The position of this curve along the abscissa depended on reaction conditions and could be characterized by c½, the
Cd2+concentration corresponding to half the maximum
A440(Fig 2) The value of c½was determined manually and found to be 1.20 ± 0.06 mMunder the standard conditions (0.37 mgÆmL)1enzyme concentration, 0.1Mionic strength,
20C) used for the experiment described in Fig 2 Among the factors tested, ionic strength, which was adjusted by the addition of KCl, had the greatest effect on c½ When the ionic strength was increased to 0.16, 0.2 and 0.6M, the c½increased to 2.6 ± 0.1, 3.0 ± 0.2 and 11 ± 1 mM, respectively, indicating that increased ionic strength de-creased the tendency of the protein to aggregate This observation suggested that the aggregation is governed by ionic forces, a finding supported by the temperature dependence of this process, in that c½ decreased from 1.20 ± 0.06 mM at 20C to 0.8 ± 0.1 mMat 2C The effect of PPase concentration on c½was moderate, in that the latter increased to 1.70 ± 0.09 mMat 0.08 mgÆmL)1PPase Specificity of the aggregation
Cd2+-induced aggregation was quite specific to E coli PPase No aggregation of the homologous yeast pyrophos-phatase was observed at Cd2+concentrations up to 11 mM
[17,18], a finding confirmed by us (data not shown) Because
of its specificity, the aggregation could be used as a simple and efficient step in PPase purification We found that the addition of 4.5 mMcadmium acetate to an E coli extract freed from nucleic acids [19] quantitatively precipitated PPase; the higher cadmium acetate concentration was required because of a low concentration of PPase in the extract This precipitated PPase could be subsequently dissolved in Cd2+-free buffer This aggregation step resulted
in a sixfold purification of PPase, with an increase of specific activity from 26 to 150 IUÆmg)1, and a yield of 90% Thus, only small amounts of other proteins in the E coli extracts were co-precipitated with PPase
PPase aggregation was also quite specific with respect to the divalent metal ion used Of the other metal ions tested, only Cu2+ and Zn2+ induced aggregation, but their effective concentrations were much higher than that of
Cd2+ (Table 1) No aggregation was observed in the presence of the PPase cofactors Mg2+ and Mn2+ and the PPase inhibitor Ca2+, all of which bind to PPase The nature of the anionic counterion (acetate or chloride) in the metal salt had no effect on c½
Identification of the metal-binding site
E coli PPase possesses three types of metal-binding sites Type 1 sites, of which there are two per monomer in the absence of substrate, are found in the active site cavity and are not involved in intersubunit or intermolecular contacts [12,13] Type 2 sites, of which there are 0.5 per monomer, are found in the intersubunit contact region; each of these sites has ligands – Asn24 and Asp26 – from two subunits
Fig 1 Time-course of Escherichia coli inorganic pyrophosphatase
(PPase) aggregation in the presence of 2 m M cadmium acetate.
Fig 2 Dependence of Escherichia coli inorganic pyrophosphatase
(PPase) aggregation on cadmium acetate concentration Absorbance
values were measured 3 min after each metal salt addition The line
was obtained with the following equation: A 440 ¼ 1.03/(1 + 9.34/
[Cd2+]12).
FEBS 2004 Aggregation of pyrophosphatase (Eur J Biochem 271) 3065
Trang 3within the same hexamer [12,13] Metal binding to type 2
sites strongly modulates trimer–trimer interactions in
hexa-meric PPase [22] Type 3 sites, of which there are six per
hexamer, are found on the surface of the enzyme molecule
and are formed by the Glu139 side-chain and backbone
oxygens and the Val150 backbone oxygen [23] (Fig 3)
We ruled out the involvement of type 1 and type 2 sites in
Cd2+-induced aggregation by testing the effects of Mg2+
and Mn2+ Both of these divalent cations bind to type 1 and
2 sites, with dissociation constants ranging from 0.076 to
6.6 mM for Mg2+and from 0.006 to 0.35 mM for Mn2+
[11] Neither Mg2+nor Mn2+, however, binds to type 3
sites [12,13] As neither Mg2+nor Mn2+aggregated PPase
(Table 1), they would be expected to increase the c½for
Cd2+ because of simple competition if the aggregating
Cd2+ ion binds to type 1 or type 2 sites We actually
observed the opposite effect, in that c½, which was
2.6 ± 0.1 mMin the absence of Mg2+and Mn2+(0.16M
ionic strength), decreased to 2.0 ± 0.1 mMin the presence
of either 20 mMMg2+or 20 mMMn2+ Our finding, that
Mg2+ and Mn2+ ions potentiated the effects of Cd2+,
indicates that aggregation is caused by Cd2+binding to sites
other than types 1 and 2
The lack of competition between Cd2+ and the other
metal ions in inducing aggregation suggested that
aggrega-tion is governed by type 3 sites This finding was supported
by our results on PPase variants with specific mutations at the metal-binding sites (Table 2) A mutation at the peripheral type 3 site (E139Q) markedly increased c½
(Table 2) and slowed down the aggregation (Fig 1) By contrast, mutations at the intersubunit site (N24D, D26N and D26S) had no effect on c½ or aggregation kinetics, although they stimulated (N24D) or eliminated (D26N and D26S) Mg2+binding to this site [22] Based on these data,
we conclude that Cd2+binding to type 3 sites is responsible for PPase aggregation
Possible mechanism One possible explanation of the Cd2+effect on PPase is that the Cd2+ binds to peripheral metal-binding sites from different hexamers, i.e Cd2+serves as a bridging atom Structural analysis predicts, however, that although this
Cd2+ion is located on the protein surface, it may not be available to bind another hexamer without inducing signi-ficant structural alterations around the metal-binding site
A more probable alternative is that Cd2+binding to the peripheral metal-binding site strengthens the intermolecular Trp149–Trp149¢ stacking interaction observed in PPase crystals [10] Trp149 belongs to the most flexible segment (residues 147–153) of the loop shown in Fig 3, as indicated
by high B-factor values in structures that contain no bound metal ion in the peripheral binding site [9,10,12,13] This segment also contains Val150, one of the metal ligands Therefore, a bound metal ion would act to fix the 147–153
Fig 3 A stereo view of the hexamer–hexamer contact observed in Escherichia coli inorganic pyrophosphatase (PPase) crystals [23] The bound Ca2+ ion is shown as a black sphere, and its coordination bonds are shown as dashed lines Unprimed and primed amino acid residue numbers and metal ions refer to two different subunits from two neighboring hexamers.
Table 2 The effects of residue substitutions on c ½ for Escherichia coli inorganic pyrophosphatase (PPase) aggregation by cadmium acetate The values for the parameter describing the titration curve (c ½ ) were measured as described in the legend of Fig 2.
PPase variant c ½ (m M )
Table 1 Comparison of different metal ions in their ability to aggregate
Escherichia coli inorganic pyrophosphatase (PPase) and general
chem-ical parameters The most commonly occurring coordination numbers
and respective ionic radii are separated by / The preferred
coordi-nation numbers are shown in bold The values for the parameter
describing the titration curve (c ½ ) were measured as described in
Fig 2.
Metal salt c ½ (m M )
Cation coordination number [20]
Cation ionic radius (A˚) [21]
CdCl 2 1.20 ± 0.06 4/5/6 0.78/0.87/0.95
ZnCl 2 6.5 ± 0.3 4/5/6 0.60/0.68/0.74
CuCl 2 13 ± 1 4/5/6 0.57/0.65/0.73
MgCl 2 > 100 6 0.72
CaCl 2 > 100 6/7/8 1.00/1.06/1.12
MnCl 2 > 100 4/5/6 0.66/0.75/0.83
3066 Y V Zimenkov et al (Eur J Biochem 271) FEBS 2004
Trang 4segment in space [23] and may adjust the position of Trp149
to allow its optimal interaction with its symmetrical partner
in the other hexamer Furthermore, the dependence of the
aggregation on [Cd2+]12in the millimolar range (Fig 2),
suggests that the corresponding Cd2+-binding constant is
well above 1 mMand that aggregate formation or growth
requires that Cd2+ should be present in at least 12
peripheral sites in the interacting enzyme molecules The
effect of ionic strength on aggregation may thus be mediated
by its effect on the Cd2+-binding constant Further studies
are, however, needed to explain the unusually strong Cd2+
concentration dependence in structural terms
The above mechanism suggests that, in order to be
effective at aggregating PPase, Cd2+would have to bind to
a type 3 binding site and properly position Trp149 These
requirements clearly impose limitations on the cation
coordination number and ionic radius The preferred
coordination number for all of the aggregating cations is
four (Cd2+can equally well adopt six ligands), whereas the
non-aggregating cations have a coordination number of six
or eight (Table 1) There is also a correlation between the
value of c½and the ionic radius within the group of the
aggregating cations However, the high value of c½
observed for Cu2+, may also result from the fact that this
cation favors square planar coordination rather than the
tetrahedral coordination favored by Cd2+and Zn2+[20]
The inability of Ca2+to aggregate PPase (Table 1), despite
its presence in the crystal structure [23], suggests that Ca2+
does not ensure proper orientation of Trp149 Indeed, even
in the crystal structure, where the neighboring protein
molecules contribute to such an orientation, the Trp149
side-chain planes are not parallel in Ca2+PPase (Fig 3)
Acknowledgements
The authors thank A N Parfenyev and I P Fabrichniy for help This
work was supported by grants from the Russian Foundation for Basic
Research (03-04-48798), the Ministry of Industry, Science and
Technologies of the Russian Federation (1706-2003-4), and the Finnish
Academy of Sciences (201611).
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