PDBsum entry 2g99

Structural protein/DNA binding protein

PDB id: 2g99

Contents

Protein chains

304 a.a. *

Ligands

ALA-ARG-THR-MLY-GLN ×2

* Residue conservation analysis

PDB id:

2g99

Name:

Structural protein/DNA binding protein

Title:

Structural basis for the specific recognition of methylated histone h3 lysine 4 by the wd-40 protein wdr5

Structure:

Wd-repeat protein 5. Chain: a, b. Fragment: residues 27-334. Synonym: bmp2-induced 3-kb gene protein, wd-repeat protein big-3, wdr5. Engineered: yes. Histone h3. Chain: c, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the dimethylated tail of histone h3 is chemically synthesized

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.212 R-free: 0.243

Authors:

J.Chai,Z.Han,H.Wang,Y.Shen

Key ref:

Z.Han et al. (2006). Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell, 22, 137-144. PubMed id: 16600877 DOI: 10.1016/j.molcel.2006.03.018

Date:

06-Mar-06 Release date: 06-Sep-06

Protein chains

P61964  (WDR5_HUMAN) -  WD repeat-containing protein 5 from Homo sapiens

Seq: 334 a.a.

Struc: 304 a.a.

DOI no: 10.1016/j.molcel.2006.03.018

Mol Cell 22:137-144 (2006)

PubMed id: 16600877

Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5.

Z.Han, L.Guo, H.Wang, Y.Shen, X.W.Deng, J.Chai.

ABSTRACT

The WD40 repeat protein WDR5 specifically associates with the K4-methylated histone H3 in human cells. To investigate the structural basis for this specific recognition, we have determined the structure of WDR5 in complex with a dimethylated H3-K4 peptide at 1.9 A resolution. Unlike the chromodomain that recognizes the methylated H3-K4 through a hydrophobic cage, the specificity of WDR5 for methylated H3-K4 is conferred by the nonconventional hydrogen bonds between the two zeta-methyl groups of the dimethylated Lys4 and the carboxylate oxygen of Glu322 in WDR5. The three amino acids Ala-Arg-Thr preceding Lys4 form most of the specific contacts with WDR5, with Ala1 forming intermolecular hydrogen bonds and salt bridges, and the side chain of Arg2 inserting into the central channel of WDR5. Both structural and biochemical studies presented here suggest another mode of recognition for the methylated histone tail.

Selected figure(s)

Figure 2.
Figure 2. The Dimethylated H3-K4 Peptide Binds to the Top Surface of the WDR40 Repeat Domain in WDR5
(A) The omit density for the dimethylated peptide and E322 in WDR5 is shown in 1.1 sigma. The residues from the peptide and WDR5 are labeled. The green arrows indicate the positions of carbonyl oxygen atoms of the peptide. The map was calculated using the program CNS.
(B) A close-up view of the surface representation of the binding channel on the top of WDR5 for the dimethylated peptide. The blue, red, and white colors represent the positive, negative, and hydrophobic surfaces of WDR5, respectively.
(C) Close-up view of the interface between the first three residues, ART, from the dimethylated peptide and WDR5. The peptide is shown using a ball-and-stick representation. The side chains of those residues from WDR5 involved interactions with the peptide are shown in magenta. The dotted lines indicate the intermolecular hydrogen bonds between WDR5 and the peptide. The two red crosses represent the two water molecules.
(D) Stereo view of the interface between the dimethylated Lys4 in the peptide and WDR5. WDR5 and the peptide are shown in orange and green, respectively.
(E) Sequence alignment among the methylation sites plus their immediately preceding three residues from the N-terminal histones. The sequence of residues RHRK is from histone H4, and all the remaining ones are from histone H3. The number after K indicates the position of Lys in histone H3 or H4.
(F) Surface representation of peptide bound WDR5 is shown in orange, and the potential HMT binding site is highlighted in magenta. Figure 2. The Dimethylated H3-K4 Peptide Binds to the Top Surface of the WDR40 Repeat Domain in WDR5(A) The omit density for the dimethylated peptide and E322 in WDR5 is shown in 1.1 sigma. The residues from the peptide and WDR5 are labeled. The green arrows indicate the positions of carbonyl oxygen atoms of the peptide. The map was calculated using the program CNS.(B) A close-up view of the surface representation of the binding channel on the top of WDR5 for the dimethylated peptide. The blue, red, and white colors represent the positive, negative, and hydrophobic surfaces of WDR5, respectively.(C) Close-up view of the interface between the first three residues, ART, from the dimethylated peptide and WDR5. The peptide is shown using a ball-and-stick representation. The side chains of those residues from WDR5 involved interactions with the peptide are shown in magenta. The dotted lines indicate the intermolecular hydrogen bonds between WDR5 and the peptide. The two red crosses represent the two water molecules.(D) Stereo view of the interface between the dimethylated Lys4 in the peptide and WDR5. WDR5 and the peptide are shown in orange and green, respectively.(E) Sequence alignment among the methylation sites plus their immediately preceding three residues from the N-terminal histones. The sequence of residues RHRK is from histone H4, and all the remaining ones are from histone H3. The number after K indicates the position of Lys in histone H3 or H4.(F) Surface representation of peptide bound WDR5 is shown in orange, and the potential HMT binding site is highlighted in magenta.

Figure 3.
Figure 3. Functional Consequences of Point Mutations in WDR5
Interaction of various WDR5 mutants with the 20 residue dimethylated peptide. A glutathione resin-mediated pull-down assay was used to assess the interaction between the 20 residue dimethylated peptide and various WDR5 mutants. The peptide dot blot analysis was used to detect the bound peptide as detailed in the Experimental Procedures. Figure 3. Functional Consequences of Point Mutations in WDR5Interaction of various WDR5 mutants with the 20 residue dimethylated peptide. A glutathione resin-mediated pull-down assay was used to assess the interaction between the 20 residue dimethylated peptide and various WDR5 mutants. The peptide dot blot analysis was used to detect the bound peptide as detailed in the [3]Experimental Procedures.

The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 137-144) copyright 2006.

Figures were selected by an automated process.