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PDBsum entry 2zkf
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References listed in PDB file
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Key reference
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Title
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Recognition of hemi-Methylated DNA by the sra protein uhrf1 by a base-Flipping mechanism.
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Authors
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K.Arita,
M.Ariyoshi,
H.Tochio,
Y.Nakamura,
M.Shirakawa.
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Ref.
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Nature, 2008,
455,
818-821.
[DOI no: ]
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PubMed id
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Abstract
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DNA methylation of CpG dinucleotides is an important epigenetic modification of
mammalian genomes and is essential for the regulation of chromatin structure, of
gene expression and of genome stability. Differences in DNA methylation patterns
underlie a wide range of biological processes, such as genomic imprinting,
inactivation of the X chromosome, embryogenesis, and carcinogenesis. Inheritance
of the epigenetic methylation pattern is mediated by the enzyme DNA
methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences
during DNA replication, depending on the methylation status of the template
strands. The protein UHRF1 (also known as Np95 and ICBP90) recognizes
hemi-methylation sites via a SET and RING-associated (SRA) domain and directs
Dnmt1 to these sites. Here we report the crystal structures of the SRA domain in
free and hemi-methylated DNA-bound states. The SRA domain folds into a globular
structure with a basic concave surface formed by highly conserved residues.
Binding of DNA to the concave surface causes a loop and an amino-terminal tail
of the SRA domain to fold into DNA interfaces at the major and minor grooves of
the methylation site. In contrast to fully methylated CpG sites recognized by
the methyl-CpG-binding domain, the methylcytosine base at the hemi-methylated
site is flipped out of the DNA helix in the SRA-DNA complex and fits tightly
into a protein pocket on the concave surface. The complex structure suggests
that the successive flip out of the pre-existing methylated cytosine and the
target cytosine to be methylated is associated with the coordinated transfer of
the hemi-methylated CpG site from UHRF1 to Dnmt1.
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Figure 2.
Figure 2: Overall structure of the SRA–hemi-methylated CpG DNA
complex. a, Ribbon representation of the SRA–DNA complex in
the same orientations as in Fig. 1a: grey, SRA; orange, N-tail
and finger loop; light blue, loop L3; light green, DNA; magenta,
flipped-out base 5mC[7]. b, Schematic representation of the
protein–DNA interactions observed in the crystal structure.
Hydrogen bonds between SRA and DNA are shown by red lines:
dotted, main-chain contacts; solid, side-chain contacts. Van der
Waals contacts between SRA and DNA are shown by blue lines. W,
water molecules mediating indirect interactions.
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Figure 3.
Figure 3: Specific recognition of a hemi-methylated CpG site by
SRA. The colour codes for the protein and DNA are same as in
Fig. 2a. Red dotted lines show hydrogen-bond contacts within 4
Å. a, Close-up view of the flipped-out 5mC[7] recognition
site. The composite-omit electron density map for 5mC[7] (more
than 6.0  )
is shown in blue. b, The orphaned guanidine G[7]' base is
retained near a canonical position in the DNA duplex by
interactions with the SRA residues. c, Interactions between the
G8  C8'
base pair adjacent to the flipped-out base and the SRA residues.
Wat, water. d, The model of fully methylated DNA bound to the
SRA. The methyl group of 5mC[8]' (shown as a green sphere)
causes steric interference with Asn 494 (orange spheres) in the
finger loop. The hydrogen-bond distances between these bases and
the SRA residues are listed in Supplementary Tables 2 and 3.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2008,
455,
818-821)
copyright 2008.
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