PDBsum entry 2k3y

Transcription regulator

PDB id: 2k3y

Contents

Protein chain

134 a.a. *

* Residue conservation analysis

PDB id:

2k3y

Name:

Transcription regulator

Title:

Solution structure of eaf3 chromo barrel domain bound to histone h3 with a dimethyllysine analog h3k36me2

Structure:

Chromatin modification-related protein eaf3. Chain: a. Fragment: unp residues 1 to 115. Synonym: esa1-associated factor 3. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: eaf3, ypr023c, yp9367.03c. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

G.Mer,C.Xu

Key ref:

C.Xu et al. (2008). Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S. Structure, 16, 1740-1750. PubMed id: 18818090 DOI: 10.1016/j.str.2008.08.008

Date:

19-May-08 Release date: 16-Sep-08

Protein chain

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

Seq: 401 a.a.

Struc: 134 a.a.*

* PDB and UniProt seqs differ at 20 residue positions (black crosses)

DOI no: 10.1016/j.str.2008.08.008

Structure 16:1740-1750 (2008)

PubMed id: 18818090

Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S.

C.Xu, G.Cui, M.V.Botuyan, G.Mer.

ABSTRACT

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.

Selected figure(s)

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).

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.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1740-1750) copyright 2008.

Figures were selected by the author.