Reference:
Li, 1995. Crystal structure of the MATa1/MATalpha2 homeodomain
heterodimer bound to DNA Science 270, 262-269. [Medline
abstract]
Click this button to color
the structure according to the tutorial below and as for Fig.
1 of the reference.
I. Introduction
The A1/alpha2 - DNA Complex exhibits several properties which
are important in DNA protein interactions:
a1 and alpha2 regulate yeast mating type loci:
So MCM1 and a1 can change binding specificity of alpha2.
All are homeodomain proteins- originally discovered in Drosophila
homeotic genes, a gene family with a conserved 60 aa sequence
near the C-terminus (the homeodomain). Many have been shown
to regulate development in various organisms. They belong to the
"helix-turn-helix" class of DNA binding proteins and
often act in combination with other homodomain proteins. The "helix-turn-helix"
proteins have an alpha helix which fits into the major groove
of the DNA, backed by 2 alpha helices which lay across the groove.
Both a1 and alpha2
bind DNA by themselves, but with low affinity and specificity.
Both binding specificity and affinity are increased 105-fold
when they bind as a homeodimer. Binding is dependent on presence
of both binding sites at proper spacing.
The sequences above are sites to which the a1/alpha2 heterodimer binds in vivo.
The boxed regions are conserved in at least 75% of the yeast binding
sites for MATa1/alpha2. Note that the conserved regions are spaced
the same distance apart at all sites.
II. The complex
The crystal structure of the a1/alpha2 heterodimer complexed with
DNA is shown at left, similar to Fig1a of the reference. To make
the coloring match the refernce and the rest of the figures of
this tutorial, click this button
. The a1 protein is shown
in cyan, the alpha2 in red,
and the DNA in yellow. In other figures, the DNA will be shown
as yellow and magenta strands. Note that the axis of the DNA double
helix is bent. This is caused by an increased roll angle of the
bases, which in turn cause a narrowing of the minor groove. Click
this button to see
the distances between phosphates across the minor groove. The
distances vary up to 2-fold. A graph of the groove widths and roll
angle for each base is shown below.
The helix bends in the direction of the protein to facilitate
binding. The combination of an a1 and
alpha2 binding site, flanking
a region of DNA of the proper length which can bend, leads to
the formation of a high affinity complex. The a1
and alpha2 proteins bind to
similar sites in the major groove of the DNA. The binding sites
are so similar that the authors transposed the figure legends
describing the binding sites in figure 6B andD. Red-Blue stereo picture of Fig1.
III. Protein-protein interaction
The a1/alpha2 protein-protein interaction can be seen by clicking here . A hydrophobic patch of the a1 homeodomain interacts with hydrophobic residues of the alpha2 C-terminal tail. Note the way the hyrophobic amino acids interdigitate between the two proteinThis interaction resembles the Oct1/VP16 interaction; these proteins share homology with a1/alpha2 in this region (see alignment above). Mutation of the hydrophobic residues to A results in loss of a1/alpha2 binding activity, based on an in vivo reporter gene assay. H-bonds, shown as dotted lines here, also contribute to this interaction.
IV. Protein-DNA contacts
A diagram of the DNA-protein contacts is shown below. H-bonds
are indicated by arrows, and the proteins are color coded as above.
Water molecules involved in H-bonds are shown as blue "w"
s. Conserved nucleotides are shown in green.
This button colors the structure as
in fig 6B, showing interactions of a1
with the major groove of the DNA. N51 forms 2 H-bonds with A26
of the DNA. This interaction is conserved in all homeodomain proteins,
including alpha2 (below).
Also conserved, but not shown, is an H-bond between R53 and the
phosphate of A4. R55 makes 2 H-bonds with G25, an interaction
similar to the N51-A26 interaction. Many other H-bonds are made
through ordered water molecules. Since water can act as both an
H donor and acceptor, these types of interactions are difficult
to predict in the absence of crystallographic data. Red-Blue stereo picture of this view.
This button Shows the interactions
of alpha2 with the major groove,
as in fig. 6D. N51 of alpha2
makes the conserved interaction with an adenosine residue, in
this case A38. R54 makes H-bonds with G6 and to N51 of alpha2 itself. S50 makes 2 water-mediated
H-bonds, one each to A4 and T5.
This button shows the interactions
alpha2 makes with the minor
groove. R4 has several potential H-bond partners. The epsilon
N can pair with N3 of A8 or A38. The terminal amine can make water
mediated bonds with G6 and C39. It is also close enough to make
a direct bond with O2 of C39. The backbone NH of glycine5 donates
an H-bond to T37, and R7 donates an H-bond to A35 and T11. Red-Blue stereo
picture of this view.
DNA mutation figure
DNA binding assay on mutant operators
alpha2 mutant has same binding specificuty as wildtype
a1 mutations affect specificity, alpha2 has effects on residual activity
Crystal structure of yeast nucleosome core particle
Figure of differences from metazoans