p53 Core Domain Bound to DNA
Jane Robertson '08 and Allison Mauk '08
As a transcription regulator, p53 plays a fundamental
role in controling cell growth. The activation of
p53 consistantly results in apoptosis. This function
is necessary to help maintain healthy levels of cell proliferation.
When p53 becomes mutated, the ability to induce apoptosis is
compromised. Thus, p53 mutations frequently result in
uncontrolled cell growth leading to tumors. Therefore,
understanding the structure, DNA-binding mechanism and mutational
characteristics is of utmost importance within the medical community.
Overall, p53 is a large tetramer protein, with identical subunits.
Each subunit contains an N-terminal transactivation domain, a
DNA-binding core domain (p53DBD), a tetramerization domain and a
C-terminal regulatory domain . However, due to the
complexity of this protein, it has not been crystallized in its
entirety. This tutorial will focus on the DNA-binding core
The crystal structure obtained by Ho et al. was
prepared from Mus musculus.
There are high levels
sequence alignment bewteen the
p53DBD of Mus musculus and the p53DBD that has
been isolated in humans. Alignment
The structural implications of the high level of sequence conservation
between mice and humans can be observed when the two structures are
the p53DBD is
isolated from the rest of the p53 protein, it is found as a dimer
However, in the presence of the
entire p53 complex and bound to DNA, it is suggested that the p53DBD
undergoes a quaternary structure alteration to a dimer of dimers.
Each of the subunits binds to the DNA nearly symmetrically and opposite
of each other via two recognition helices
dimerization contacts are formed through a Zinc
domain which is positioned over the minor
the site of dimerization, a 20°
in the DNA is formed.
However, this effect was not observed in a monomer of p53DBD that was
crystallized bound to DNA. This suggests that it is the actual
formation of the dimer that induces this bend.
subunit is made up of a sandwich of
β-sheets and two
H1 is involved in the dimer-dimer interactions
whereas H2 is responsible for DNA recognition and binding. There
are also a number of loop regions, most
Another loop, the L1 region, shows a large amount of flexibility
between species which has led to the suggestion that it is in no way
involved with DNA binding. L1
In this particular paper, the L1 loop was unable to be crystallized
which is likely a result of its flexibility.
between p53DBD and
DNA are mediated through the H2 recognition helix, the proceeding loop
region, and the L3
alpha helix interacts with the DNA major groove at the decamer
consensus sequence for the p53 recognition site.
The decamer consensus sequence for the
recognition of the p53 dimer follows a very simple pattern of
PuPuPuC(A/T|A/T)GPyPyPy, where Pu indicaties a purine and Py indicates
a pyrimadine. All p53 response elements contain similar decamer
the H2 helix, Arg
277 binds with
guanosine 7 in
the DNA major groove.
Arg 277 makes DNA backbone contacts, as
Ala 276 and
Within the L3 loop region,
interact with the DNA minor groove
explained above, a zinc atom is fundamental in maintaining the
structure of the p53 protein structure. This zinc atom binds
the H1 helix and L3 loop of the protein. These two motifs are
fundamental in the dimer interactions that maintain the stability of
the p53 dimer.
der Waals, hydrogen bonding, and electrostatic interactions.
Van der Waals interactions are made between Pro-174
H1 helices of opposing subunits of the dimer
Additionally, there are intermolecular salt
bridges resolved between Arg-178
both of which are also on the H1 helices of the
there are hydrogen bonds
other bonds display dipole-dipole and electrostatic interactions
between Arg-178 and Glu-177 on each subunit
known the the p53
protein interacts with
DNA as a dimer of dimers, or a tetramer.
Unfortunately, this structure
has not yet been crystallized. Based on the crystalized
the p53 dimer, Ho et al. created a model of the
tetramer-DNA complex (Ho
et al. Model). These two
dimers interact in a tail to tail mechanism, whereas the DNA-bound
dimer functions through head to head interactions.
p53 mutations in cancer cells
methods, including lesions that prevent p53 activation, mutations
mutations of downstream mediators of p53 function. Regardless
how p53 becomes mutated, the mutation generally has drastic
consequences. About half of all cancers display a p53
There are two classes
mutations that occur in p53: contact mutants and conformational
mutants. Affecting the amino acids required to maintain the
structure of the p53 dimer, conformational mutants are found primarily
in the H1 helix and L3 loop of the protein
Contact mutants are mutations found near the
protein-DNA interface, especially in the H2 helix
are the residues most frequently found to be
mutated in cancer. More specifically, Cho et al.
determined there are
six “hotspot” mutations
These residues—five arginines
and one glycine—are
specific mutations most commonly seen in cancer. Arg-248
is the most
common, accounting for 9.6% of p53 mutations
The other most commonly mutated
residues are Arg-273
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six residues are all highly
involved at the p53-DNA binding interface. Arg-248 makes contact at the
minor groove, while Arg-273 contacts a phosphate on the backbone of the
DNA. The four other residues are all involved in stablizing the
structure of the DNA-binding surface of p53.
Svetlana Forina, Philip D. Jeffrey, Nikola P. Pavletich. 1994. Crystal
Structure of a p53 Tumor Suppressor-DNA Complex: Understanding
Tumorigenic Mutations. Science
 Ho, William C., Mary X. Fitxgerald, Ronen
Marmorstein. 2006. Structure of the p53 Core Domain Dimer Bound to DNA.
Journal of Biological
Chemistry 281: 20494-20502.
Akhelesh K., Victor B. Zhurkin, Steward R. Durell, Robert L. Jernigan,
Ettore Apella, Rodney E. Harriington. 1999. p53-induced DNA bending and
twisting: p53 tetramer binds on the outer side of a DNA loop and
increases DNA twisting. Proc. Natl. Acad. Sci. 96:
 Vousden, Karen H., Xin Lu. 2002. Live or Let
The Cell's Response to p53. Nature