Originally published In Press as doi:10.1074/jbc.M109815200 on December 11, 2001
J. Biol. Chem., Vol. 277, Issue 7, 5448-5452, February 15, 2002
The SCAN Domain of ZNF174 Is a Dimer*
James R.
Stone
§,
Jenny L.
Maki
,
Stephen C.
Blacklow§, and
Tucker
Collins
§¶
From the Departments of Pathology,
Children's
Hospital and § Brigham & Women's Hospital, Harvard Medical
School, Boston, Massachusetts 02115
Received for publication, October 10, 2001
 |
ABSTRACT |
The SCAN domain is a conserved region of 84 residues found predominantly in zinc finger DNA-binding proteins in
vertebrates. The SCAN domain appears to control the association of SCAN
domain containing proteins into noncovalent complexes and may be the primary mechanism underlying partner choice in the oligomerization of
these transcription factors. Here we have overexpressed, purified, and
characterized the isolated SCAN domain (amino acids 37-132) from
ZNF174. Both size exclusion chromatography and equilibrium sedimentation analysis demonstrate that the ZNF174 SCAN domain forms a
homodimer. Circular dichroism shows that the isolated SCAN domain dimer
has ~42%
-helix. Thermal denaturation experiments indicate that
the SCAN domain undergoes a single reversible unfolding transition with
a Tm of over 70 °C. The midpoint of the equilibrium unfolding transition increases with increasing protein concentration, consistent with a two-state unfolding transition in
which folded dimer is in equilibrium with unfolded monomer. These
findings demonstrate that the isolated SCAN domain forms a stable dimer
and support a model in which the SCAN domain is capable of mediating
the selective dimerization of a large family of vertebrate-specific,
zinc finger-containing transcription factors.
 |
INTRODUCTION |
Transcription factors are composed of modular elements that
include a DNA-binding domain and one or more separable effector domains
that activate or repress transcription. Other modules within these
factors regulate subcellular localization and gene expression by
mediating selective association of the transcription factors with each
other, or with other cellular components. Identification of these
domains often provides a conceptual framework for understanding the
function of the transcription factor.
The SCAN1 domain is a highly
conserved vertebrate-specific protein domain found in ~60 genes in
the human genome (1, 2). Only a handful of these gene products have
been characterized thus far, and they appear to control a wide range of
biological processes including development, cell differentiation, and
lipid metabolism (reviewed in Refs. 3 and 4). The name for the SCAN
domain was derived from the first letters of the names of four proteins
initially found to contain this domain (SRE-ZBP, CTfin51, AW-1 (ZNF174), and Number
18 cDNA or ZNF197) (5). Alternatively, this domain has been
referred to as LeR for leucine-rich domain (6). The SCAN domain
consists of an 84-residue, leucine-rich region and is predicted to
contain a high degree of
-helix. It is located at the N
terminus when it is part of a zinc finger-containing transcription
factor. The primary amino acid sequence of the domain does not
resemble any of the other zinc finger-associated domains, such as the
Kruppel-associated box (KRAB) or the poxvirus and zinc finger (POZ)
domain, which is also known as the BTB (Broad-complex, Tramtrack, and
Bric-a-brac) domain (7-9). Members of the SCAN domain family are
broadly expressed and appear to function as either activators or
repressors of transcription. The SCAN domain in isolation generally
does not affect transcription.
In previous studies we and others (10-12) demonstrated that the SCAN
domain functions as an oligomerization domain, mediating self-association or association with other proteins bearing SCAN domains. In part of those studies, a fragment of the N terminus of
either ZNF174 or ZNF202 that encompassed the SCAN domain behaved as an
oligomeric species. However, in those studies the definitive subunit
stoichiometry of the oligomeric SCAN domain was not determined. Here we
have utilized the sequences of the 60 SCAN domains in the human genome
to more completely define the limits of the domain. We have
overexpressed, purified, and characterized the isolated SCAN domain
from ZNF174. Gel filtration, sedimentation equilibrium, and thermal
denaturation studies demonstrate that the isolated SCAN domain forms a
stable homodimer. These findings support a model in which the SCAN
domain is capable of mediating the selective dimerization of a large
family of vertebrate-specific, zinc finger-containing transcription factors.
 |
EXPERIMENTAL PROCEDURES |
Plasmid Construction--
The DNA segment containing residues
37-132 of ZNF174 was amplified from a full-length clone of ZNF174
using polymerase chain reaction. This amplified fragment was then
subcloned into the BamHI site of pGEX-2T (Amersham
Biosciences, Inc.). Automated dideoxynucleotide sequencing of
the SCAN domain insert verified the correct orientation and
authenticity of the insert. The predicted protein product consists of
the SCAN domain insert fused with glutathione S-transferase
(GST). The amino acid sequence of the final protein product after
cleavage from GST with thrombin consists of the 96-residue sequence
illustrated in Fig. 1, preceded by glycine-serine. This 98-residue
protein has a calculated isoelectric point of 8.7 and a
molecular mass of 11.56 kDa.
Bacterial Expression and Purification of the SCAN
Domain--
Escherichia coli BL21 bacteria transformed with
the pGEX-SCAN fusion construct were grown to an
A600 of 0.6 at 37 °C and then induced
with 0.1 mM
isopropyl-
-D-thiogalactopyranoside for 1-2 h. The cells
were pelleted at 4000 × g for 30 min. The cells were then suspended in phosphate-buffered saline (67 mM
phosphate, 150 mM NaCl, 5 mM DTT, pH 7.4, or
phosphate-buffered saline, 30 ml/1 liter of culture) containing
0.1% Nonidet-P40 (Roche Molecular Biochemicals) and Complete protease
inhibitor mixture (1 tablet/50 ml, Roche Molecular Biochemicals). The
cells were lysed by sonication, and the homogenate was centrifuged at
3000 × g for 30 min. Glutathione-Sepharose 4B
(Amersham Biosciences, Inc.) was added to the resulting supernatant (0.75 ml resin/1 liter of culture). The supernatant was then agitated on a rocker for 20 min and then centrifuged at 500 × g
for 5 min. The resulting supernatant was removed, and the resin was
placed in a chromatography column and washed with 2 bed volumes of
phosphate-buffered saline. The resin was then incubated as a 50%
slurry with thrombin (80 units/0.75 ml of resin) at 25 °C overnight.
The resin was then washed with one bed volume of phosphate-buffered
saline, and the eluate was diluted 1:2 with water.
All subsequent steps were performed at 4 °C using a Biologic HR
chromatography system (Bio-Rad). The sample was applied at 1 ml/min to
an S5 cation exchange column (Bio-Rad). The column was washed with 34 mM phosphate, 75 mM NaCl, and 5 mM
DTT, pH 7.4, and then the protein was eluted with a linear NaCl
gradient running from 75 mM to 1 M in 34 mM phosphate, 5 mM DTT, pH 7.4. The sample was
then concentrated to 0.5 ml with a Centricon YM-3 (Amicon, 3000 Da
MWCO) at 3000 × g. The sample was then applied to a
Bio-Prep S.E.-100/17 size exclusion chromatography column (8 × 300 mm, Bio-Rad) equilibrated in 25 mM phosphate, 200 mM NaCl, 1 mM DTT, pH 6.5, at a flow rate of
0.2 ml/min.
Analytical Size Exclusion Chromatography--
Recombinant
purified SCAN domain (225 µM subunit) in 25 mM phosphate, 200 mM NaCl, 1 mM
DTT, pH 6.5 was applied a Bio-Sil SEC 250-5 analytical gel filtration
column (Bio-Rad) at 0.7 ml/min with a back-pressure of 800 p.s.i. using a Biologic HR chromatography system (Bio-Rad). The
column was calibrated under the same conditions with the following
protein standards (thyroglobulin, molecular weight 670,000; IgG,
158,000; ovalbumin, 44,000; myoglobin, 17,000).
Sedimentation Equilibrium--
The isolated SCAN domain was
dialyzed overnight against 25 mM phosphate, 200 mM NaCl, 1 mM DTT, pH 6.5. Sedimentation
equilibrium was performed at 20 °C in a Beckman XL-A Analytical
Ultracentrifuge using three rotor speeds (16,000, 21,000, and 26,000 rpm) and at three different protein concentrations (5, 15, and 50 µM subunit). After samples had reached equilibrium
(typically 18 h), they were scanned in triplicate at 280, 236, and
229 nm. Data were analyzed with a linear least squares fitting
program (KaleidaGraph) using a partial specific volume of 0.738 calculated using
WEBTools.2
CD Spectroscopy--
CD spectra were recorded at 4 °C
on an Aviv 62DS spectropolarimeter equipped with a thermoelectric
temperature controller. Samples of recombinant ZNF174-isolated SCAN
domain (25 µM subunit) were prepared in 25 mM
phosphate, 200 mM NaCl, 0.2 mM DTT, pH 6.5. Spectra representing the average of five scans from 260 to 195 nm were
measured in a 1-mm path length cuvette, using a step size of 1 nm and a
3-s signal-averaging time. All spectra were corrected for the base line
obtained with the buffer alone.
Thermal Denaturation--
Thermal denaturation was performed by
monitoring the molar ellipticity at 222 nm of the SCAN domain at
various temperatures. Experiments were performed with protein
concentrations of 2 and 5 µM subunit in a cuvette with a
1-cm path length. Measurements were made with a 2-min equilibration
time and a 2 °C step interval. The melting temperature
(Tm) for each protein concentration was determined
from the peak position on the plot of
d
222 nm/d(1/T) versus
T.
Secondary Structure Predictions--
The predicted secondary
structure for the isolated SCAN domain was determined using the
following on-line prediction programs: PredictProtein, PREDATOR,
nnPredict, Hierarchical Neural Network, Prof, Jpred, and
SSpro.3
Miscellaneous Methods--
The purity of the protein was
assessed by SDS-polyacrylamide electrophoresis using an XCell Surelock
electrophoresis cell (Novex) and 4-12% precast gradient gels.
N-terminal sequencing and matrix-assisted laser desorption mass
spectrometry (MALDI-MS) of the purified SCAN domain was performed by
the University of Michigan, Protein Core Facility, Ann Arbor, MI.
Protein concentrations were determined using the Bradford microassay
(Bio-Rad) with bovine serum albumin as the standard. The SCAN domain
sequences were aligned using the ClustalW alignment program in
MacVector, version 6.5.3.
 |
RESULTS |
Defining the Limits of the SCAN Domain--
Analysis of the Celera
human genome data base has revealed the presence of ~60 genes
containing the SCAN domain
(1-3).4 An alignment of a
select number of these members is illustrated in Fig.
1 (5, 12-19). There is clear homology
starting with E-43 of ZNF174 and extending to R-126 of ZNF174. Below
the sequences is a compilation of the predicted secondary structure
based on several publicly available programs, with "H"
corresponding to a residue predicted to be in an
-helix by all of
the programs, and "h" corresponding to a residue
predicted to be in an
-helix by some but not all of the programs.
The secondary structure prediction algorithms predict three to five
-helices within the SCAN domain. Based on the sequence alignment,
the secondary structure prediction, and the biochemical properties of
the recombinant protein detailed below, the SCAN domain is being
defined as 84 residues, beginning with E-43 and ending with R-126 of
ZNF174. In addition, there are frequently one or more proline residues
just before and after the domain.

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Fig. 1.
The SCAN domain. Ten of the 60 SCAN
domains present in humans have been aligned with dark
gray and light gray backgrounds used to indicate
identical or conserved residues, respectively. The numbers
at the top of the alignment indicate the amino acid
positions in ZNF174. Underneath the sequences is the
predicted secondary structure, with "H" representing a
residue predicted to be in an -helix by all of the programs used and
"h" representing a residue predicted to be in an
-helix by some but not all of the programs used. The SCAN domain is
defined as 84 residues extending from E-43 to R-126 in ZNF174.
|
|
Purification of the Isolated SCAN Domain from ZNF174--
In
initial studies we examined the behavior of an N-terminal region of
ZNF174 that contained the SCAN domain (10). Collectively, these
previous studies, as well as work by others with the SCAN domain of
ZNF202 (11), demonstrate that the SCAN domain behaves as an oligomeric
species under near physiologic conditions. However, the precise subunit
stoichiometry of the oligomeric SCAN complexes was not determined. To
better define the nature of the SCAN domain, we over-expressed and
purified to homogeneity only the isolated SCAN domain (amino acids
37-132) from ZNF174 (Fig. 2). The
98-residue recombinant protein consists of the 96 residues illustrated
in Fig. 1, preceded by glycine-serine. The protein was prepared as a
GST fusion, affinity-purified, cleaved with thrombin to remove the GST,
and then subjected to cation exchange and size exclusion chromatographies (Fig. 2A). The protein preparation yields
about 0.3 mg/liter of bacterial cell culture. The composition of the recombinant protein was verified by both N-terminal sequencing (GSKN)
and MALDI-MS (predicted 11560 Da; observed 11562 Da).

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Fig. 2.
Purification of recombinant SCAN domain.
A, 4-12% gradient SDS-polyacrylamide gel. Lane
1, protein standards; lane 2, supernatant; lane
3, GST-Sepharose affinity-purified GST-SCAN domain fusion protein
before thrombin cleavage; lane 4, eluate containing SCAN
domain after cleavage with thrombin; lane 5, SCAN domain
after cation exchange chromatography; lane 6, SCAN domain
after size exclusion chromatography. B, analytical size
exclusion chromatography of the purified SCAN domain. Recombinant
purified SCAN domain (225 µM subunit) in 25 mM phosphate, 200 mM NaCl, 1 mM
DTT, pH 6.5, was applied to an analytical gel filtration column. The
column was calibrated under the same conditions with the following
protein standards: thyroglobulin, 670,000 Da, 8.9 min; IgG, 158,000 Da,
11.2 min; ovalbumin, 44,000 Da, 12.5 min; myoglobin 17,000 Da, 14.5 min. The indicated positions for monomer, dimer, and trimer were
determined from a linear regression of the standards using a
subunit molecular mass of 11.56 kDa for the SCAN domain.
|
|
The SCAN Domain Forms Dimers--
The recombinant SCAN domain was
subjected to analytical size exclusion chromatography. The protein
eluted as a single peak with a retention time of 13.8 min (Fig.
2B). The following molecular mass standards were employed:
myoglobin, 17 kDa, 14.5 min; ovalbumin, 44 kDa, 12.5 min; IgG, 158 kDa,
11.2 min; and thyroglobulin, 670 kDa, 8.9 min. Based on a plot of the
logarithm of the molecular mass of the protein standards
versus the retention time, the molecular mass of the
recombinant SCAN domain was determined to be 23.6 kDa. Because the
subunit molecular mass is 11.56 kDa, the result indicates that the
recombinant SCAN domain is a dimer.
Given that knowledge of the precise subunit stoichiometry of oligomeric
SCAN is critical for understanding its function, the native molecular
mass of the recombinant SCAN domain was further assessed by
sedimentation equilibrium. Sedimentation equilibrium is generally
considered the definitive method for determining the native molecular
mass of an oligomeric protein in solution, as it assesses the protein
in solution at equilibrium (20). Unlike gel filtration and
velocity-sedimentation based measurements, sedimentation equilibrium
analysis is independent of the shape of the molecule. The defining
characteristic of sedimentation equilibrium is the concentration
gradient that forms at equilibrium as the flux of sedimenting protein
is exactly balanced by the flux of diffusing molecules. The analysis
was performed at three rotor speeds (16,000, 21,000, and 26,000 rpm)
and three different protein concentrations (5, 15, and 50 µM). Absorbances were recorded at three
wavelengths (229, 236, and 280 nm) in triplicate. When the natural log
of the absorbance is plotted against the square of the radius, a linear
plot is obtained, the slope of which allows for the calculation of the
native molecular mass of the oligomer. A representative plot at a rotor
speed of 16,000 rpm and at a protein concentration of 50 µM is shown in Fig.
3A. Also on this plot are the
calculated lines that would result for a protein with a subunit mass of
11.56 kDa and with oligomeric subunit stoichiometries of 1, 2, or 3. The residuals from a best fit of the plotted data are shown in Fig.
3B. The calculated subunit stoichiometry for each protein
concentration is depicted in Fig. 3C. The values were
averaged over the three acquisitions and for the three different rotor
speeds. The sedimentation equilibrium results clearly demonstrate that
the isolated SCAN domain is a dimer.

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Fig. 3.
Sedimentation equilibrium analysis of the
SCAN domain. Sedimentation equilibrium analysis of the recombinant
SCAN domain from ZNF174 was performed using a Beckman XL-A Analytical
Ultracentrifuge with three different protein concentrations in 25 mM phosphate, 200 mM NaCl, 1 mM
DTT, pH 6.5, at 20 °C. A, a representative log plot from
a sample containing 50 µM (subunit) SCAN centrifuged at
16,000 rpm. Shown with the data are the calculated lines that would
result for a protein with a subunit mass of 11.56 kDa and with
oligomeric subunit stoichiometries of 1, 2, or 3. B, the
residuals from a linear regression of the data shown in
A above. C, the calculated subunit stoichiometry
for each protein concentration. The values were averaged over three
separate acquisitions for each of three different rotor speeds. The
error bars represent two standard deviations.
|
|
The SCAN Dimer Has High Thermodynamic Stability--
CD spectra of
the recombinant isolated SCAN domain shows that the protein has a high
degree of secondary structure (Fig.
4A). Analysis of the spectra
reveals that the SCAN domain has about 42%
-helix. These values are
in good agreement with secondary structure predictions described above,
which yield estimations of helical content ranging from 36 to 63%.

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Fig. 4.
CD spectroscopy of the SCAN domain. CD
spectroscopy of the purified SCAN domain was performed in 25 mM phosphate, 200 mM NaCl, 0.2 mM
DTT, pH 6.5. A, CD spectrum of the isolated SCAN domain of
ZNF174 (25 µM subunit) at 4 °C. B, thermal
denaturation of the SCAN domain of ZNF174. The molar ellipticity at 222 nm at increasing temperatures was determined for the SCAN domain at
either 5 µM subunit (closed circles) or 2 µM subunit (open circles).
|
|
Thermal denaturation of the isolated SCAN domain was performed to
investigate the stability of the SCAN dimer. The loss of negative
ellipticity at 222 nm was monitored by CD spectroscopy as the
temperature was increased. This analysis shows that unfolding is
sigmoidal and single phase (Fig. 4B). The protein is
surprisingly stable, with a melting temperature (Tm)
of 75 °C at 5 µM subunit. The thermal denaturation was
reversible with the same Tm as for unfolding and
with 94% of the negative ellipticity at 222 nm recovered upon stepwise
lowering of the temperature. As a consequence of the dimeric structure
of the SCAN domain, the apparent stability should depend upon the
protein concentration. In fact, as the protein concentration is
decreased, the Tm is shifted to a lower temperature
(72 °C with 2 µM subunit). This trend is consistent
with a two-state model in which folded dimer is in equilibrium with
unfolded monomer.
 |
DISCUSSION |
To minimize the possible proaggregatory effects of residues
outside the actual SCAN domain, sequences of the 60 SCAN domains from
the human genome were aligned to more clearly define the limits of the
domain. In addition, secondary structure predictions were used to help
predict where structural elements may begin and end. Based on this
analysis the domain is defined as 84 residues extending from E-43 to
R-126 in ZNF174. In many sequences, there are proline residues both
before and after the domain, which helps to delineate the boundaries of
the predicted secondary structural elements. The secondary structure
prediction algorithms predict the presence of three to five
-helices
in the domain. The limits for the domain described here are in good
agreement with those listed in two on-line domain data
bases.5 In Prosite the domain
is defined as ZNF174 residues 46-128, and in Pfam the domain is
defined as ZNF174 residues 40-135. The third on-line domain data base,
SMART (which refers to the domain as LER), currently defines the domain
as ZNF174 residues 42-154. However, the additional ~25 residues at
the C terminus show much less homology than those within the domain as
defined here. These additional residues are clearly not required for
the formation of a stable recombinant protein, as they are lacking in
the construct employed here. Thus, it is concluded that the SCAN domain
extends from E-43 to R-126 (in ZNF174) and is frequently flanked by one or more proline residues on both ends.
SCAN domain proteins have been shown by in vitro
co-expression studies to form homo- and hetero-oliogomers (10-12).
Previous studies on recombinant polypeptides containing SCAN domains
have also shown these proteins to be oligomers (10, 11). However, in
both of these studies, the precise oligomeric subunit stoichiometry was
not clear, as the recombinant proteins demonstrated a retention time on
gel filtration significantly shorter than would be expected for a
simple dimeric species. However, in contrast to these previous studies,
the protein employed here was a stable dimer not only on gel filtration
but also by definitive sedimentation equilibrium analysis. This
construct was designed to minimize nonspecific interactions
(i.e. aggregation) and thus has allowed for the definitive determination of the subunit stoichiometry. Furthermore, the molecule used here was well behaved biophysically as evidenced by reversible thermal denaturation. The high degree of stability of the SCAN dimer,
as indicated by the Tm of over 70 °C, is ideal for a protein that may serve as a dimerization domain, as is the case
with BTB/POZ (21) and with the leucine zippers of GCN4, FOS, and JUN
(22, 23).
These studies indicate that the isolated SCAN domain forms dimers and
suggests that the SCAN domain is utilized as a dimerization domain by
multidomain zinc finger-containing transcription factors. However, most
of the proteins in the SCAN family contain multiple zinc fingers, which
could presumably enable them to bind DNA as monomers. Thus, a key
question concerns why these transcription factors may need to dimerize
for proper biological function. Analysis of the human genome indicates
that there are ~60 SCAN-containing transcription factors present
(1-3).4 Furthermore, SCAN appears to be a
vertebrate-specific (if not mammal-specific) domain. Given that
there are 60 SCAN domain-containing proteins in humans and that the
SCAN domain can dimerize, it then follows that there are 1830 possible
dimeric complexes that could result from these 60 human genes (not
accounting for alternatively spliced forms). However, because in
vitro co-expression studies have suggested that there is
selectivity in homo- and heterodimer formation (10-12), not all of the
1830 possible combinations may actually exist. Nonetheless, the
introduction of the SCAN domain within a defined set of zinc
finger-containing transcription factors allows for a potentially large
diversity in the number of transcription factors available to the
species. Complex organisms may require this diversity in transcription
factors for development and homeostasis. Investigations to determine
the structural characteristics regulating selective homo- and
heterodimer formation are in progress.
 |
FOOTNOTES |
*
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
Pathology, Children's Hospital, 300 Longwood Ave., Boston, MA 02115. Tel.: 617-355-5806; Fax: 617-734-4721; E-mail:
tcollins@rics.bwh.harvard.edu.
Published, JBC Papers in Press, December 11, 2001, DOI 10.1074/jbc.M109815200
2
Found on the Web at
bmb.psu.edu/nixon/WEBTools/mwtvbar.htm.
3
Found on the Web, respectively, at:
dodo.cpmc.columbia.edu/ predictprotein/;
embl-heidelberg.de/cgi/predatorserv.pl;
cmpharm.ucsf.edu/~nomi/nnpredict.html; npsa-pbil.ibcp.fr/cgi-bin/npsaautomat.pl?page=npsann.html;
aber.ac.uk/~phiwww/prof/; jura.ebi.ac.uk:
8888/; promoter.ics.uci.edu/BRNN-PRED/.
4
T. Sander, J. R. Stone, J. L. Maki,
and T. Collins, unpublished observations.
5
Prosite is found at
expasy.ch/cgi-bin/nicesite.pl?PS50804, Pfam at
sanger.ac.uk/cgi-bin/Pfam/getacc?PF02023, and SMART at smart.
embl-heidelberg.de/.
 |
ABBREVIATIONS |
The abbreviations used are:
SCAN, SRE-ZBP, CTfin51, AW-1 (ZNF174),
and Number 18 cDNA or ZNF197;
DTT, dithiothreitol;
GST, glutathione S-transferase;
MALDI-MS, matrix-assisted laser
desorption mass spectrometry.
 |
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