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PDBsum entry 2k3y
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Transcription regulator
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PDB id
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2k3y
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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 for the recognition of methylated histone h3k36 by the eaf3 subunit of histone deacetylase complex rpd3s.
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Authors
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C.Xu,
G.Cui,
M.V.Botuyan,
G.Mer.
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Ref.
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Structure, 2008,
16,
1740-1750.
[DOI no: ]
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PubMed id
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Abstract
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Deacetylation of nucleosomes by the Rpd3S histone deacetylase along the path of
transcribing RNA polymerase II regulates access to DNA, contributing to faithful
gene transcription. The association of Rpd3S with chromatin requires its Eaf3
subunit, which binds histone H3 methylated at lysine 36 (H3K36). Eaf3 is also
part of NuA4 acetyltransferase that recognizes methylated H3K4. Here we show
that Eaf3 in Saccharomyces cerevisiae contains a chromo barrel-related domain
that binds methylated peptides, including H3K36 and H3K4, with low specificity
and millimolar-range affinity. Nuclear magnetic resonance structure
determination of Eaf3 bound to methylated H3K36 was accomplished by engineering
a linked Eaf3-H3K36 molecule with a chemically incorporated methyllysine analog.
Our study uncovers the molecular details of Eaf3-methylated H3K36 complex
formation, and suggests that, in the cell, Eaf3 can only function within a
framework of combinatorial interactions. This work also provides a general
method for structure determination of low-affinity protein complexes implicated
in methyllysine recognition.
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Figure 1.
Figure 1. Solution NMR Structures of Eaf3 in the Free State
and Linked to Histone H3K[C]36me2
(A) Left: Stereo view of
the 20 lowest-energy structures of Eaf3 chromo barrel domain
(1–113 aa) showing only backbone N, C^α, and C′ after
superposition of residues 8–41 and 55–111. The rmsd is 0.54
and 1.16 Å for the backbone atoms N, C^α, and C′ and
for all heavy atoms of residues 8–41 and 55–111,
respectively. Right: Ribbon representation of the lowest-energy
structure of Eaf3 chromo barrel domain. The helices (α) and β
strands (β) are colored green and blue, respectively. N and C
termini are also indicated.
(B) Left: Stereo view of the 20
lowest-energy structures of Eaf3-H3K[C]36me2 (1–134 aa)
showing only backbone N, C^α, and C′ after superposition of
residues 8–41, 55–111, and 127–130. The Eaf3 chromo barrel
domain (1–115 aa) is colored black, while the linker
(116–119 aa) and H3K[C]36me2 (120–134 aa) are shaded blue
and orange, respectively. The rmsd is 0.61 and 1.13 Å for
the backbone atoms N, C^α, and C′ and for all heavy atoms of
residues 8–41, 55–111, and 127–130, respectively. Right:
Cartoon representation of the lowest-energy structure of
Eaf3-H3K[C]36me2; ribbon for Eaf3 and stick for a portion of
H3K[C]36me2. The helices (α) and β strands (β) are indicated.
Color coding is the same as in (A).
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Figure 4.
Figure 4. Details of Eaf3 Chromo Barrel Domain Interaction
with the Linked Histone H3K[C]36me2 Sequence
(A) Chemical
conversion of a cysteine residue to a dimethyllysine analog
(K[C]me2).
(B) Close-up view of the main interaction site
within the Eaf3-H3K[C]36me2 protein. Tyr23, Tyr81, Trp84, and
Trp88 of the chromo barrel domain of Eaf3 form an aromatic cage
that accommodates the linked dimethylated lysine analog of
H3K36. Other residues (Leu21 and Lys85 of Eaf3; and V35 and
Pro38 of linked H3K[C]36me2) involved in the interaction are
also labeled.
(C) Planes from the 3D ^15N nuclear
Overhauser effect spectroscopy (NOESY) experiment showing NOE
correlations of W88HE1 of Eaf3 to K[C]36me2, Lys37, and Pro38 of
linked H3K[C]36me2 (left); and ^13C-edited NOESY experiments
showing NOE correlations of W88HE3 of Eaf3 to K[C]36me2, Lys37,
and Pro38 of linked H3K[C]36me2 (middle), and NOE correlations
of the HD protons of P38 of linked H3K[C]36me2 to the aromatic
protons of Trp84 and Trp88 of Eaf3 (right).
(D) Stereo view
of the superposition of 10 NMR structures each of free Eaf3
(blue) and Eaf3-H3K[C]36me2 complex (Eaf3 in green and
H3K[C]36me2 in orange) showing a close-up representation of the
aromatic pocket binding site.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Structure
(2008,
16,
1740-1750)
copyright 2008.
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