 |
PDBsum entry 3e9f
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transcription
|
PDB id
|
|
|
|
3e9f
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Molecular basis of the interaction of saccharomyces cerevisiae eaf3 chromo domain with methylated h3k36.
|
|
|
Authors
|
|
B.Sun,
J.Hong,
P.Zhang,
X.Dong,
X.Shen,
D.Lin,
J.Ding.
|
|
|
Ref.
|
|
J Biol Chem, 2008,
283,
36504-36512.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Abstract
|
|
|
Eaf3 is a component of both NuA4 histone acetyltransferase and Rpd3S histone
deacetylase complexes in Saccharomyces cerevisiae. It is involved in the
regulation of the global pattern of histone acetylation that distinguishes
promoters from coding regions. Eaf3 contains a chromo domain at the N terminus
that can bind to methylated Lys-36 of histone H3 (H3K36). We report here the
crystal structures of the Eaf3 chromo domain in two truncation forms. Unlike the
typical HP1 and Polycomb chromo domains, which contain a large groove to bind
the modified histone tail, the Eaf3 chromo domain assumes an autoinhibited
chromo barrel domain similar to the human MRG15 chromo domain. Compared with
other chromo domains, the Eaf3 chromo domain contains a unique 38-residue
insertion that folds into two short beta-strands and a long flexible loop to
flank the beta-barrel core. Both isothermal titration calorimetry and surface
plasmon resonance studies indicate that the interaction between the Eaf3 chromo
domain and the trimethylated H3K36 peptide is relatively weak, with a K(D) of
approximately 10(-4) m. NMR titration studies demonstrate that the methylated
H3K36 peptide is bound to the cleft formed by the C-terminal alpha-helix and the
beta-barrel core. Site-directed mutagenesis study and in vitro binding assay
results show that the conserved aromatic residues Tyr-23, Tyr-81, Trp-84, and
Trp-88, which form a hydrophobic pocket at one end of the beta-barrel, are
essential for the binding of the methylated H3K36. These results reveal the
molecular mechanism of the recognition and binding of the methylated H3K36 by
Eaf3 and provide new insights into the functional roles of the Eaf3 chromo
domain.
|
|
|
|
|
|
|
|
Figure 1.
Structure of the Eaf3 chromo domain. A, overall structure and
electrostatic surface of the short form Eaf3 chromo domain
(residues 1–113). B, overall structure and electrostatic
surface of the long form Eaf3 chromo domain (residues 1–124).
The C-terminal part forms a stable α-helix in both structures.
The Eaf3 chromo domain contains a 38-residue insertion (shown in
red), which, together with the β-barrel core, forms a long,
deep surface groove. C, sequence comparison of the chromo domain
from yeast Eaf3, human MRG15, and Drosophila HP1. Strictly
conserved residues are highlighted in shaded red boxes, and
conserved residues are highlighted in open red boxes. The
secondary structure of the Eaf3 chromo domain is placed above
the alignment. D, structural comparison of the Eaf3 chromo
domain (cyan, insertion in red) with the MRG15 (gray, Protein
Data Bank code 2F5K) and HP1 (purple, Protein Data Bank code
1KNA) chromo domains. Residues forming the hydrophobic pocket
are shown with side chains. The bound peptide in the HP1 chromo
domain complex is shown in magenta.
|
|
Figure 2.
Characterization of the Eaf3 chromo domain binding to histone
H3 peptides. A, characterization of binding of the Eaf3 chromo
domain with various histone H3 peptides using isothermal
titration calorimetry: H3K36me3 peptide (a); H3K36me2 peptide
(b); H3K36 peptide (c); H3K4me3 peptide (d); H3K4me2 peptide
(e); H3K9me3 peptide (f). The upper panels show the raw data for
injections of the peptides into the Eaf3 chromo domain, and the
lower panels show the integrated heats of the injections. B,
binding of the short form Eaf3 chromo domain with the H3K36me3
peptide measured by ITC and SPR. C, binding of the long form
Eaf3 chromo domain with the H3K36me3 peptide measured by ITC and
SPR. RU, response units. D, binding of the wild-type and mutant
Eaf3 chromo domain with the H3K36me2 peptide using in vitro
binding assay. Negative control 1 (N1) shows that the H3K36me2
peptide does not have nonspecific binding with the nickel beads;
negative control 2 (N2) shows that the Eaf3 chromo domain does
not have nonspecific reaction with the anti-H3K36me2 antibody;
positive control (P) shows the specific binding between the
H3K36me2 peptide and the anti-H3K36me2 antibody.
|
|
|
|
|
|
The above figures are
reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2008,
283,
36504-36512)
copyright 2008.
|
|
|
|
|
|
|
