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PDBsum entry 1s4z
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Gene regulation
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PDB id
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1s4z
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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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Structural basis of hp1/pxvxl motif peptide interactions and hp1 localisation to heterochromatin.
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Authors
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A.Thiru,
D.Nietlispach,
H.R.Mott,
M.Okuwaki,
D.Lyon,
P.R.Nielsen,
M.Hirshberg,
A.Verreault,
N.V.Murzina,
E.D.Laue.
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Ref.
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EMBO J, 2004,
23,
489-499.
[DOI no: ]
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PubMed id
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Abstract
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HP1 family proteins are adaptor molecules, containing two related chromo domains
that are required for chromatin packaging and gene silencing. Here we present
the structure of the chromo shadow domain from mouse HP1beta bound to a peptide
containing a consensus PXVXL motif found in many HP1 binding partners. The
shadow domain exhibits a novel mode of peptide recognition, where the peptide
binds across the dimer interface, sandwiched in a beta-sheet between strands
from each monomer. The structure allows us to predict which other shadow domains
bind similar PXVXL motif-containing peptides and provides a framework for
predicting the sequence specificity of the others. We show that targeting of
HP1beta to heterochromatin requires shadow domain interactions with
PXVXL-containing proteins in addition to chromo domain recognition of
Lys-9-methylated histone H3. Interestingly, it also appears to require the
simultaneous recognition of two Lys-9-methylated histone H3 molecules. This
finding implies a further complexity to the histone code for regulation of
chromatin structure and suggests how binding of HP1 family proteins may lead to
its condensation.
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Figure 2.
Figure 2 Structure of the HP1  shadow
domain/CAF-1 complex. (A) The backbone of residues 110 -172 of
HP1 and
214 -232 of CAF-1 from the 25 lowest energy structures (out of
72 that converged from the 100 computed). The structure has good
covalent geometry and nonbonded contacts (Table 1). The peptide
backbone around residues Asp-214 -Glu-219 of CAF-1 is not well
defined in the structure because only the Phe-217 and Ile-218
side chains interact with the shadow domain. 15N relaxation
studies show that the peptide backbone in this region has
increased mobility within the complex when compared to residues
in the PXVXL motif (Figure 1A). (B) The structure closest to the
mean, rotated by 90° about the z-axis, compared to the
orientation shown in (A). This structure is compared with that
of the free shadow domain (PDB code: 1DZ1; Brasher et al, 2000)
and the chromo domain/histone H3 complex (PDB code: 1GUW;
Nielsen et al, 2002). In the structure of the free shadow
domain, the side chains of Trp-170, which stabilise the position
of the C-terminal tails, are shown. (C) Stereoview of the
structure closest to the mean showing side chains of residues
involved in the HP1 /CAF-1
peptide interface. (D, E) Close-up views of the interactions
made by (D) Val-224 (position 0) and (E) Pro-222 and Leu-226
(positions -2/+2), Phe-217/Ile-218 (-7/-6 positions) and
Ile-229/Leu-230 (+5/+6 positions). In (A -D), the HP1 monomers
are coloured blue and magenta and the CAF-1 peptide is coloured
green. (Note: Trp-170 is not shown on monomer A because it does
not interact with Leu-226 at the +2 position.) 
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Figure 3.
Figure 3 Shadow domain alignment in which the residues involved
in complex formation are highlighted (numbering is for mouse HP1
).
Residues important for recognition of the PXVXL motif are
highlighted in yellow (Val-224) and red (Pro-222/Leu-226 at the
-2/+2 positions). Residues that form the hydrophobic patch that
interacts with the flanking N- and C-terminal sequences
(Phe-217/Ile-218 and Ile-229/Leu-230 at the -6/-7 and +5/+6
positions, respectively) are highlighted in blue. Residues that
are not conserved and are predicted to alter specificity are
boxed. Conserved residues that define the fold of the shadow
domain are highlighted in grey, while residues important for
dimerisation are indicated by blue triangles. Phe-163 (indicated
by a green dot) is important for both the structure of the
shadow domain and peptide binding. The positions of secondary
structure elements in mouse HP1 are
indicated by purple arrows ( -strands)
and cylinders (  -helices)--the
dots indicate the positions of the conserved bulges in the first
strand. Sequences are labelled by species name (Mm--Mus
musculus, Hs--Homo sapiens, Gg--Gallus gallus, Xl--Xenopus
laevis, Dm--Drosophila melanogaster, Dv--Drosophila virilis,
Os--Oryza sativa, Zm--Zea mays, At--Arabidopsis thaliana,
Dc--Daucus carota, Sp--Schizosaccharomyces pombe,
Ec--Encephalitozoon cuniculi, Ce--Caenorhabditis elegans,
Le--Lycopersicon esculentum).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2004,
23,
489-499)
copyright 2004.
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