Structure
and Function of
DNA Methyltransferase 1
Willie Miller-Little & Austin Griffin
Contents:
I.
Introduction
DNA
methylation
is
important for the epigenetic regulation of genes, through
silencing.
Maintenance of such methylation, in mammals,
is primarily mediated by DNA methyltransferase1-(DNMT1).
DNMT1 is a 1620 residue protein composed of a CXXC
domain
,two
Bromo-adjacent-homology
(BAH) domains,
and
a DNA
containing methyltransferase
domain,
which
also contains a Target
recognition
domain (TRD).
The crystal
structures of both the mouse and the
Human DNMT1 protein have been solved.
These two proteins share 85% sequence identity
and share very
similar
structures. This protein functions by
the CXXC domain binding specifically to hemimethylated CpG
nucleotides,
and
interacts in such a way that the CXXC-BAH1 linker between DNA
and the protein’s active site,
preventing de novo methylation. It also
performs an autoinhibitory mechanism in which unmethylated CpG sites
are
occluded from the active site, selecting for Hemimethylated CpG
dinucleotides.
II.
CXXC Domain
The
CXXC domain (residues 650-699)
contains a crescent like fold.
This
single domain makes all sequence specific interactions with the DNA.
These
interactions target both the major and the minor groove, and contain a
4Bp
footprint. The Major groove interactions are made between the
Arg684
Ser685
Lys686
Gln687 which
form a loop segment
that penetrates the major groove,
making
hydrogen bonds.
Lys686
and
Gln687
contact the Guanine bases
via hydrogen bonds
in the unmethylated dinucleotide
Ser685
Lys686
interact
with the cytosine bases.
However,
these are not the only
interactions made with the
DNA, the CXXC
domain also contains recognition sites of salt bridges
from arginines
to the
phosphodiester backbone of the DNA
. The CXXC
domain also aids
in the control of not interacting with Methylated CpG sites.
This control
occurs due to steric
hindrance. If a methyl group were
present on the CpG
dinucleotide, it would
unfavorably interact with (Arg684
Ser685
Lys686 ) due to steric
interference with nearby peptide atoms
.
III.
BAH Domains
The BAH1 and
BAH2
domains adopt a common fold similar to the Orc1p BAH domain.
These
domains are connected by an alpha helix (BAH linker)
and form a dumbbell like configuration
,
and
are both
physically associated with the methyltransferase domain. The BAH1
domain
is anchored to the linker alpha helix by a Cys3His-coordinated
Zn2+
ion,
while the BAH2 domain loop is anchored
to the TRD
of the
methyltransferase domain
.
IV.
Methyl Transferase
The
Methylt transferase domain in DMNT1 is the
main catalytic domain of the protein. It contains two
subdomains, the
Target recognition domain (TRD), and the catalytic core, which are
separated by
a large cleft in the protein, which is occupied by the DNA.
The catalytic
core is composed of seven mixed β-sheets
.
flanked on either side by
three A-helices
.
The
DNA in mDNMT1 complex is anchored by the
CXXC domain, withdrawn from the DNMT1 active site.
Unmethylated DNA is
occluded from the active site because f the autoinhibitory function of
the
CXXC-BAH1 linker (highlight and zoom, rotate). The CXXC-BAH1
linker
contains a highly acidic segment spanning residues D703-D711
[Figure
3D.]
and
is positioned between the DNA and the active
site .
The BAH2-TRD loop also
anchors the
TRD in a retracted position, preventing major groove interactions with
the DNA. These
two activities function to prevent
unmethylated Cpg dinucleotides from entering the active site, and only
allows
hemimethylated dinucleotides to enter the active site.
V.
References
1.
J.A. Law, S.E.
Jacobsen, Nat. Rev. Genet. 11, 204 (2010).
2.
X. Cheng, R.M. Blumenthal, Structure 16, 341 (2008).
3.
M. G. Goll, T.H. Bestor, Annu.
Rev. Biochem. 74, 481 (2005).
4. Song J. et. al. Structure of DNMT1-DNA Complex Reveals a
Role for Autoinhibition in Maintenance DNA Methylation. Science
vol. 331. (25, February, 2011 )
5. Watson,
James D. Molecular
Biology of the Gene 3d Ed.with Ill.by Keith Roberts. 6th
ed.
Menlo Park,Calif: W.A.Benjamin, 1976.
Back to Top