SAGE-Hindawi Access to Research
Journal of Amino Acids
Volume 2011, Article ID 812540, 7 pages
TheDynamicStructureof the EstrogenReceptor
RajKumar,1Mikhail N. Zakharov,2ShaguftaH.Khan,1Rika Miki,3HyeranJang,2
1Department of Basic Sciences, The Commonwealth Medical College, Scranton, PA 18510, USA
2Section of Endocrinology, Boston University School of Medicine, Boston, MA 02118, USA
3Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
4Division of Endocrinology and Metabolism, Charles Drew University of Medicine and Science, Los Angeles, CA 90059, USA
Correspondence should be addressed to Ravi Jasuja, email@example.com
Received 1 April 2011; Accepted 6 June 2011
Academic Editor: Faizan Ahmad
Copyright © 2011 Raj Kumar et al. This is an open access article distributed under the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
its site-specific DNA and with other coregulatory proteins. In recent years, new information regarding the dynamic structural
nature of ER has emerged. The physiological effects of estrogen are manifested through ER’s two isoforms, ERαand ERβ. These
two isoforms (ERαand ERβ) display distinct regions of sequence homology. The three-dimensional structures of the DNA-binding
domain (DBD) and ligand-binding domain (LBD) have been solved, whereas no three-dimensional natively folded structure for
and how the structural features of the two isoforms differ, and its subsequent role in gene regulation.
The estrogen receptor (ER) is a ligand-inducible intracellular
transcription factor that mediates most of the biological
effects of estrogens at the level of gene regulation [1–3].
Estrogen biology is exceedingly complex and important in
iological phenomena [4–6]. In the nucleus, the ER up- or
downregulates the expression of target genes by interacting
through its site-specific DNA and with other coregulatory
proteins that include coactivators and corepressors [1–3].
The ligand-bound ER binds as homodimer to specific DNA
sequences termed estrogen response elements (EREs) and
regulates transcription through interaction with transcrip-
machinery . In recent years, new information regarding
the ER structures, intra- and intermolecular interactions,
posttranslational modifications, and several other factors
pertaining to the ER actions has emerged [8–10]. Like other
members of the nuclear hormone receptor (NHR) family,
the ER is composed of several functional domains that serve
DNA-binding domain (DBD); (3) ligand-binding domain
(LBD). Two activation function (AF) domains, AF1 and
AF2, located within the NTD and LBD, respectively, are
responsible for regulating the transcriptional activity of ER
 (Figure 1(a)).
Full transcription activity of the ER is thought to be
achieved by synergism between the two AFs, and their ac-
tivities are promoter and cell specific . AF1 functions as
hormone independent, whereas AF2 function requires the
presence of hormone/steroid [12, 17]. In this paper, we focus
on the two isoforms of human ER (ERα(NR3A1) and ERβ
(NR3A2)), encoded by two different genes. Both have been
cloned and characterized . The physiological effects of
estrogen are manifested through both ERαand ERβ. The ERα
and ERβ receptor isoforms display distinct tissue distribu-
tions and signaling response [19–21]. ERαand ERβhave also
been shown to form hetero dimers on EREs . In terms
of sequence homology, the ERβshows a high homology to
ERαin the DBD (more than 95% amino acid identity) and
2 Journal of Amino Acids
LBD (E) (F)
DBD (C)(D)LBD (E)(F)
1 144 227 255
DBD + ERE
Figure 1: (a) shows the sequence organization of the two isoforms of estrogen receptors, ERαand ERβ. Different domains are highlighted
in different colors: NTD—amino terminal domain—in red; DBD—DNA binding domain—in green; hinge region—in blue; LBD—ligand-
binding domain—in yellow; F region located towards the C-terminal end—in grey. Amino acid sequence position is given for each domain.
(b) shows estrogen receptor DBD in complex with DNA-ERE (estrogen response element). Structure 1HCQ from PDB (protein databank)
. (c) shows 3-dimensional structures of ERα(left) and ERβ(right) bound to estradiol (PDB structures 1A52  and 3OLS ).
in the LBD (∼55% amino acid identity) [19, 22]. However,
the NTD of ERβ is shorter than that of ERα with a very
poor sequence homology of only ∼15% compared to that of
ERα. The three-dimensional structures of the independently
expressed DBD and LBD have been solved and show overall
folds that represent globular proteins with natively ordered
conformations [13, 23–25]. To date, no three-dimensional
natively folded structure for the NTD is available not only
for the ER but for the entire nuclear hormone receptor
(NHR) superfamily. Even though the full length structure of
the peroxisome proliferator-activated receptor-γ (PPAR-γ)
has been solved, it failed to show any signature of structure
formation in its NTD . Warnmark et al. have previously
provided insights about the structural and functional corre-
lations regarding the ER NTD . In this paper, we discuss
the knowledge about the structural characteristics of the ER
and its role in gene regulation.
2.The Hinge Region
The “D” domain which follows DBD is known as a hinge
region (Figure 1(a)). It contains nuclear localization signal
which gets unmasked upon ligand binding and serves as a
flexible region connecting DBD and LBD. Hinge regions of
ERαand ERβshare only 36% homology .
3.The “F” Region
The LBD is followed by the C terminal “F” domain, which
contains 42 amino acids. Its action was first characterized
by Montano et al. by single-point mutations in the domain
as well as by whole domain deletion . The “F” domain
manner. The ligand, promoter, and tissue-specific modula-
tion capabilities of the “F” domain were recently studied in
detail by Koide et al. . It is also known to impact receptor
Like other NHRs, the “E” domain of ER contains LBD
(Figure 1(a)). It consists of 12 helices, contains hormone
binding pocket, and is responsible for the most part of func-
to AF2  and dimerization interface. While ERαand ERβ
have both overlapping and unique functions, the overall ho-
mology between the ERαprotein LBD and ERβprotein LBD
does not exceed 55% . However, the two proteins (ERα
and ERβ) display distinct regions of sequence homology
[4, 19]. The amino acid residues 223–343 and 404–457 in
ERα and ERβ show a significantly higher homology than
that of the sequence encompassing 223–457 and 344–403,
respectively . Interestingly, the stretch of the ER LBD
amino acid residues 465–468, with lowest homology to ERβ,
has been found to be most solvent accessible . On the
other hand, the conserved regions with greater homology are
protected against degradation and are in direct contact with
the ligand . Despite low sequence homology in LBDs
within the NHR superfamily, the three-dimensional struc-
Journal of Amino Acids3
Both isoforms of ER-LBDs have been shown to form dimers
with agonist and antagonist ligands. The dimer interface is
primarily encompassed by helices 10 and 11.
As a member of the NHR superfamily of transcription
factors, ERαcontains a globular LBD structure that harbors
a hormone-binding site, a homo- or heterodimerization in-
terface, and coregulator (activator and repressor) interaction
sites [35–38]. The ERαLBD structure contains 11 α-helices
(H1–H12) [24, 39] (Figure 1(c)). The first crystal structure
of an ERαLBDbound to its naturalligand 17β-estradiol (E2)
showed that in a compact ellipsoid cavity, E2 is buried in
a highly hydrophobic environment . Within this pocket
(formed by 22 residues), hydroxyl groups in estradiol at
positions 3 and 17 play a crucial role in orienting the steroid/
hormone ligand. These hydroxyl groups of the A and D rings
are hydrogen bonded to Glu353 from H3, Arg394 from H5,
and a water molecule and His524 from H11. In an agonist-
bound form, ERα is spatially organized in a three-layered
structure with helices 4, 5, 6, 8, and 9 lining up on one
side by H1 and H3, and on the other side are helices 7, 10,
and 11 . Due to the central role of estrogen signaling
in diverse diseases ranging from cancer to aging, several
synthetic ligands to ERαhave been developed [40–43]. The
crystal structure of the complex of ERαLBD bound to the
nonsteroidal ligand, diethylstilbestrol, also shows that the
hydrophobic interactions primarily govern the accommoda-
tion of distinct LBD structures .
The crystal structures of the human ERβ bound to
genistein , estradiol  (Figure 1(c)), and rat ERβ to
raloxifene  assert the importance of hydrogen bond
network on the opposite sides of the respective ligands .
The bicyclic moiety of genistein orients in a position similar
to the C- and D-ring of E2, facilitating the formation of hy-
drogen bonds of hydroxyl moieties with histidine groups of
the receptor . The specificity of the ligand association
between the ERα and ERβ may stem from the distinction
in the residues lining the binding pocket . Quite diverse
family of compounds (estrogens, some androgens, phytoe-
strogens, antiestrogens, and environmental estrogens) have
been shown in the past to have estrogenizing activity, and
to interact with the ER from rat uterus and human breast
tumor cells. Interactions of these structurally diverse ligands
highlight the intrinsic ERαand ERβLBD plasticity [47–49].
5.The DNA-Binding Domain
Adjacent to the N-terminal transactivation region (A/B do-
sequence . This DNA-binding domain associates with
the response elements which can either reside proximally to
the promoter regions or enhancer regions located distant
from the transcription initiation site . ER DNA bind-
ing domain usually binds to the estrogen response ele-
ment (ERE) composed of a palindromic hexanucleotide
5?AGGTCAnnnTGACCT3?[51–53]. The DBD of both ERα
and ERβisoforms shares the same DNA response elements.
The ERE sequences play an important regulatory role [54,
55]. Not only does it dictate the binding affinity of the ER,
but also it has been shown to modulate the recruitment of
coactivators [56, 57]. The ERα DBD:ERE structures have
been studied extensively by several biophysical techniques
[13, 23, 55, 58]. Three-dimensional structure of the ERαhas
been solved using nuclear magnetic resonance as well as X-
ray crystallographic techniques both alone and in complex
with DNA (Figure 1(b)) [13, 23, 55, 58]. The DBD:ERE
interactions and ERE-facilitated dimerization are in part
mediated through the P box and D box sequences in the Zinc
finger domains. These Zn finger subdomains are comprised
of 8 cysteine residues that coordinate with the two Zn+2ions.
While P box actively interacts with the ERE nucleotides, the
D box is present at the dimerization interface [29, 30, 54].
The specificity of ER recognition by ERE is exemplified
by interesting studies describing its association with glu-
cocorticoid response element (GRE). Three amino acids in
the first Zn finger region or ER dictate its interaction with
ERE and GRE . Substitution of these three amino acids
with the corresponding amino acids from the glucocorticoid
receptor’s DBD completely changes ER DBD’s specificity
for an ERE, and it strongly binds to a GRE sequence to
58]. Transcriptional regulation at the ERE can be mediated
via two separate mechanisms of ER action. Liganded ER
can directly associate with specific response element se-
quences. In the other mode of action, the ER may partic-
ipate in a multiprotein, preinitiation complex and regulate
sequence [59–61]. Together, these mechanisms highlight
the complex role of coactivators and response elements in
eliciting specificity in transcriptional output.
6.The N-Terminal Domain
To date relatively little information has been available on
the structure of the N-terminal regions of the NHRs.
Even though the full-length structure of the peroxisome
proliferator-activated receptor-γ (PPAR-γ) has been solved
it failed to show any signature of structure formation in
its very short NTD . We and others have shown that
the glucocorticoid receptor’s N-terminal transactivation AF1
region and a shorter core fragment of AF1, the AF1 core, are
unstructured in aqueous solution [62–66]. In other words,
dered (ID) conformation, a feature of activation domains of
have been reported for the ERα and ERβ, androgen-, and
progesterone receptor [69–71]. Thus, activation domains of
many signaling proteins including the ER’s NTD/AF1 are
known to exist in an ID state. One of the reasons for their
existence as an ID region seems to be to help them in pro-
moting molecular recognition by providing surfaces capable
of binding specific target molecules [72–75].
The computational analyses have established that under
physiological conditions, the combination of low mean hy-
drophobicity and relatively high net charge represent an
important prerequisite for the lack of well-defined compact
structure in proteins or protein regions/domains . The
4 Journal of Amino Acids
2040 60 80 100
204060 80 100120140
A summary of predicted secondary structural elements in the ER NTD
Figure 2: Secondary structural elements predictions of the ER NTD using network protein sequence analysis method as described .
Blue, red, and purple colors indicate helix, β-sheet, and random coil, respectively. The upper panel: ERα; the middle panel: ERβ. The table at
the bottom summarizes the contents of different secondary structural elements in the NTD of both ERs.
dichroism method . We performed secondary structural
analyses of the ERα and ERβ NTD using network protein
sequence analysis . The analytical results show that more
than 67% of ERαNTD contains random coli conformation,
whereas in case of ERβ, the amount of random coil is found
to be more than 80% with only a small proportion as helix
and sheet in both the cases (Figure 2). It has been proposed
“sample” its environment until appropriate concentration
and affinity of the binding partner proteins are found ,
meaning that they may not be structured until they have
either by induced-fit or selective binding of a particular con-
former, a high-affinity activation domain:binding partner
protein interaction occurs [65, 73]. In case of NHRs’ ID
NTD/AF1 domains, it has been shown that they undergo
a transition to a folded state upon interaction with either
components of the general transcription machinery or with
other comodulators .
Several coregulatory proteins are involved in the effect of
the ER on target gene transcription. The TATA box-binding
protein (TBP) has a central role in the basal transcription
machinery and can directly bind to the NTD of the ERαbut
scription . This difference in TBP binding could imply
differential recruitment of target proteins by the NTDs of
ERαand ERβ. The affinity of the ERαNTD:TBP interaction
very fast, low-affinity association, followed by a slow, folding
event and tighter association . The initial association
may be occurring by electrostatic interactions between the
positively charged TBP. However, this initial unstable protein
complex subsequently may convert into a more stable form
by the folding of the ID ERα NTD and the formation of
specific contacts between the two proteins. In this study, the
secondary structures of the independently expressed NTDs
of the ERαand ERβwere analyzed using NMR and circular
dichroism spectroscopy .
Secondary structural analyses concluded that both ERα
and ERβ NTDs are unstructured in solution . Further,
when ERαNTD was bound to TBP, structural changes were
induced in ERαNTD . These results support models of
of ERα. Further, the dissociation of this binding suggests a
complex behavior, with a rapid dissociation for ERα NTD
molecules that did not undergo proper folding and a slower
dissociation for those molecules that did fold successfully
binding mechanism is consistent with the change in protein
conformation that accompanies the ERαNTD:TBP interac-
tion. Observed differences in binding of TBP to ERαNTD
and ERβ NTD supports a model where the two receptors
may be utilizing different sets of target binding proteins .
This is consistent with the reports of functional differences
between ERαNTD and ERβNTD where it has been shown
that the ERαAF1 domain can function in an autonomous
manner, whereas the AF1 function of ERβcannot . It has
also been reported that under most conditions ERβpossesses
a weaker transactivational potency compared to ERα ,
and these differences appear to be cell and promoter specific
. We have earlier shown that TBP binding induces sec-
Journal of Amino Acids5
the glucocorticoid receptor such that AF1’s interaction with
specific coregulatory proteins and subsequent AF1-mediated
transcriptional activity is significantly enhanced [77, 78].
Based on the binding of TBP and consequent folding of
these ID activation domains, it can be hypothesized that the
functionally active conformation under physiological condi-
ate favorable protein interaction surfaces for its interaction
with specific coregulatory proteins. Of course, the exclusion
of certain other binding partners cannot be ruled out. It
could thus be hypothesized that a complex and dynamic
binding pattern for the N-terminal activation domains of the
NHRs occurs to achieve transcriptional activation, where the
NTD/AF1 region must be able to obtain different confor-
mations dependent on the binding partner(s). However, a
clear picture will emerge only when the functionally folded
three-dimensional structure of the NTD/AF1 is solved. At
least for now, the differential effects observed in case of two
ER isoforms (ERα NTD and ERβ NTD) suggests that TBP
may not be a common coregulator that must bind/fold all
the NHRs’ NTD/AF1. Thus, it is quite possible that other
protein components from the basal transcription machinery
may provide such interactions. In fact, we and others have
observed that at least in case of the androgen receptor, its
ID NTD/AF1 undergoes disorder/order transition through
its interaction with RAP74, a subunit of TFIIF, an important
component of basal transcription machinery [70, 79].
Recent observations have led to the conclusion that in cells,
ER and several other NHRs behave very dynamically such
that their kinetic behavior in cells allows them to rapidly
interact with various coregulatory proteins, and with chro-
matin and DNA . Further, the ER moves to various sites
in cells to function, and the local concentrations and various
other constellations of potential coregulatory proteins are
required to associate with the ER to activate or repress the
expression of target genes . The LBD crystal structures
have clearly demonstrated that differing sets of coactiva-
tors/corepressors come together in response to agonist or
antagonist ligand binding, such that agonist in one cell type
can be an antagonist in another cell type. The overall picture
is one of a complex, dynamic network controlled by the ER.
It is not yet clear whether unique tissue/cell-specific coreg-
ulatory protein interactions can fully explain the tissue/cell-
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