The Estrogen Receptor

Estrogen is a steroid hormone, and because of is structure (which is the same framework as cholesterol) it is able to diffuse through the cell membrane and bind to its receptor which in turn acts on the target genes. The focus in this tutorial is the estrogen receptor's interaction with DNA.

Properties of the Receptor

a nuclear hormone receptor
a member of the eukaryotic protein receptor super family (which includes vitamin D receptor) which is highly conserved among species
a ligand activated transcription factor
activates gene transcription by binding to the hormone response elements (HRE's) associated with target genes
binds to the consensus sequence AGGTCA NNN TGACCT

Overall structure of the receptor

This picture shows the simple structure

a pair of amphipathic alpha helices packaged at right angles which co-ordinate two Zn ions by the receptors cysteine residues.

Co-ordination of the Zn ions

    The common Zn ion co-ordination in many proteins is the Zn finger. The Zn finger has the Zn ion held by two histidines and two cysteines.
    However the Zn ions in the estrogen receptor are co-ordinated (tetrahedrally ligated) by four cysteine residues. This is known as the CLASS II Zn FINGER
      Here is another picture of the cysteines holding the Zn ions in one monomer.

Domains in the receptor

C-terminus

contains the hormone binding domain
is responsible for transactivation and dimerisation of the receptors
the part of the dimer interface is the region with the most contact.

N-terminus

transcriptional activation
nuclear localization signal

Central

DNA binding domain

Properties of the DNA binding Domain

two short alpha helix perpendicular in position hiding the hydrophobic domain
recognizes and makes contact to a 6 base pair half site AGGTCA
discrimination between other binding sites is by three amino acids Glutamic acid 25, Glycine 26 and Alanine 29. (If you mutate these residues there is no discrimination for the receptor)
recognition helix enters the major grove of the DNA.
co-ordinates a Zn ion

Binding of the Estrogen Receptor to the DNA

The movie represents the Estrogen receptor binding as a dimer to the DNA at the HRE. In in the cell the estrogen receptor is present as a monomer. It binds estrogen as a monomer, but as the movie shows, when it is going to contact the DNA it binds as a dimer. The spacer (the NNN in between the half sites) allows the DNA to bend when the receptor binds. The movie presented of this protein is showing a very springy appearance this is due to the use of the molecular simulation made by the programmes NAMD and VMD.
Here is a static picture of the estrogen receptor bound to the DNA

The role of Water

The binding estrogen receptor has to complement the surface of the DNA and this is helped by the water molecules. The water acts as an intermediate agent as it helps the protein match its surface to the surface of the DNA.
The assistance of the water is in the stabilization of the protein-DNA complex by forming hydrogen bonds at the protein-DNA interface.
The water molecules have also been found clustering the phosphate backbone of the DNA. The H-bonds here may also help in stabilizing the estrogen receptor to the DNA.
This figure was created using VMD

All these factors: water, specific side chains and the bending of the DNA work together to allow the estrogen receptor to bind specifically to the consensus sequence AGTCCA NNN TGGACT
There is still research going on in the specificity of the estrogen receptor. I hope this tutorial has given you some insight into the binding specificity of the estrogen receptor.

References and Acknowledgements

The papers used for information
Schwabe et al (1993) The crystal structure of the Estrogen receptor DNA binding domain bound to DNA: How receptor discriminate between their response elements Cell 75:567-578
Kosztin et al (1997) Binding of the Estrogen receptor to DNA. The role of waters Biophysical journal 73:557-70

Many of the pictures in this tutorial were used from
    Rasmol (courtesy of Biochemistry department UQ) and PBD files from the Protein Databank
   Pictures (as indicated) and movie courtesy of Theoretical Biophysics group at University of Illinois at Urbana-Champaign
   Indicated pictures are courtesy of Expasy/swisprot.

The work in this tutorial could not have been presented without the help from
Dr Robert Blakely
Tony Coates HTML Course
Stephen Pike