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PDBsum entry 1mvx
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of the set domain histone lysine methyltransferase clr4.
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Authors
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J.Min,
X.Zhang,
X.Cheng,
S.I.Grewal,
R.M.Xu.
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Ref.
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Nat Struct Biol, 2002,
9,
828-832.
[DOI no: ]
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PubMed id
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Abstract
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Methylation of histone H3 lysine 9 is an important component of the 'histone
code' for heterochromatic gene silencing. The SET domain-containing Clr4
protein, a close relative of Su(var)3-9 proteins in higher eukaryotes,
specifically methylates lysine 9 of histone H3 and is essential for silencing in
Schizosaccharomyces pombe. Here we report the 2.3 A resolution crystal structure
of the catalytic domain of Clr4. The structure reveals an overall fold rich in
beta-strands, a potential active site consisting of a SAM-binding pocket, and a
connected groove that could accommodate the binding of the N-terminal tail of
histone H3. The pre-SET motif contains a triangular zinc cluster coordinated by
nine cysteines distant from the active site, whereas the post-SET region is
largely flexible but proximal to the active site. The structure provides
insights into the architecture of SET domain histone methyltransferases and
establishes a paradigm for further characterization of the Clr4 family of
epigenetic regulators.
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Figure 3.
Figure 3. The active site. a, A CPK model showing the
distribution of conserved residues. Identical and similar
residues among the four proteins shown in Fig. 1a are shown in
blue and magenta, respectively. The area enclosed in the dashed
lines has the highest concentration of conserved residues. The
model is viewed in the same orientation as in Fig. 2a. b, A
surface representation of the structure. Red, blue and white
indicate negatively charged, positively charged and neutral
surface potentials. The structure is shown in the same
orientation as in (a), and the same area is enclosed by a yellow
dashed line. A blue arrow points to the cleft where Arg 406
resides. c, Stereo view of the conserved area shown in (a,b).
The side chains of several conserved residues are shown as stick
models (carbon, orange; nitrogen, blue; oxygen, red; sulfur,
magenta) superimposed with a ribbon drawing of the structure as
in Fig. 2a. Key residues are labeled.
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Figure 4.
Figure 4. Potential cofactor-binding cleft in the HMTase domain
of Clr4. A top view of the structure shown in a surface
representation. Arg 409 and Tyr 381 are located in a cleft
connected to the active site.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2002,
9,
828-832)
copyright 2002.
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