PDBsum entry 3e9f

Transcription

PDB id: 3e9f

Contents

Protein chain

99 a.a. *

Ligands

MES

Waters ×123

* Residue conservation analysis

PDB id:

3e9f

Name:

Transcription

Title:

Crystal structure short-form (residue1-113) of eaf3 chromo domain

Structure:

Chromatin modification-related protein eaf3. Chain: a. Fragment: eaf3, unp residues 1-113. Synonym: esa1-associated factor 3. Engineered: yes

Source:

Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.190 R-free: 0.217

Authors:

B.Sun,J.Hong,P.Zhang,D.Lin,J.Ding

Key ref:

B.Sun et al. (2008). Molecular Basis of the Interaction of Saccharomyces cerevisiae Eaf3 Chromo Domain with Methylated H3K36. J Biol Chem, 283, 36504-36512. PubMed id: 18984594 DOI: 10.1074/jbc.M806564200

Date:

22-Aug-08 Release date: 04-Nov-08

Protein chain

Q12432  (EAF3_YEAST) -  Chromatin modification-related protein EAF3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 401 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M806564200

J Biol Chem 283:36504-36512 (2008)

PubMed id: 18984594

Molecular Basis of the Interaction of Saccharomyces cerevisiae Eaf3 Chromo Domain with Methylated H3K36.

B.Sun, J.Hong, P.Zhang, X.Dong, X.Shen, D.Lin, J.Ding.

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.

Selected figure(s)

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.

Figures were selected by an automated process.