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The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases.

Zhang P, Lee H, Brunzelle JS, Couture JF - Nucleic Acids Res. (2012)

Bottom Line: We herein provide biochemical and structural evidence showing that WDR5 binds the Win motifs of MLL2-4, SET1A and SET1B.Comparative analysis of WDR5-Win complexes reveals that binding of the Win motifs is achieved by the plasticity of WDR5 peptidyl-arginine-binding cleft allowing the C-terminal ends of the Win motifs to be maintained in structurally divergent conformations.Overall, our findings illustrate the function of WDR5 in scaffolding the SET1 family of KMTs and further emphasize on the important role of WDR5 in regulating global histone H3 Lys-4 methylation.

View Article: PubMed Central - PubMed

Affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.

ABSTRACT
In mammals, the SET1 family of lysine methyltransferases (KMTs), which includes MLL1-5, SET1A and SET1B, catalyzes the methylation of lysine-4 (Lys-4) on histone H3. Recent reports have demonstrated that a three-subunit complex composed of WD-repeat protein-5 (WDR5), retinoblastoma-binding protein-5 (RbBP5) and absent, small, homeotic disks-2-like (ASH2L) stimulates the methyltransferase activity of MLL1. On the basis of studies showing that this stimulation is in part controlled by an interaction between WDR5 and a small region located in close proximity of the MLL1 catalytic domain [referred to as the WDR5-interacting motif (Win)], it has been suggested that WDR5 might play an analogous role in scaffolding the other SET1 complexes. We herein provide biochemical and structural evidence showing that WDR5 binds the Win motifs of MLL2-4, SET1A and SET1B. Comparative analysis of WDR5-Win complexes reveals that binding of the Win motifs is achieved by the plasticity of WDR5 peptidyl-arginine-binding cleft allowing the C-terminal ends of the Win motifs to be maintained in structurally divergent conformations. Consistently, enzymatic assays reveal that WDR5 plays an important role in the optimal stimulation of MLL2-4, SET1A and SET1B methyltransferase activity by the RbBP5-ASH2L heterodimer. Overall, our findings illustrate the function of WDR5 in scaffolding the SET1 family of KMTs and further emphasize on the important role of WDR5 in regulating global histone H3 Lys-4 methylation.

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Comparative analysis Win motif binding modes. (A) Superimposition of WDR5-bound MLL1 (beige) and MLL2 (yellow) peptides. (B) Overlay of MLL1 (beige) and MLL4 (green) peptides in complex with WDR5 (grey). (C) Structural alignment of WDR5–MLL1Win and WDR5–SET1AWin complex in which carbons of the peptides are highlighted as in Figure 2. Residues of WDR5 peptidyl-arginine-binding adopting divergent conformation between the complexes are rendered as pink carbon atoms. Hydrogen bonds and water molecules are rendered as in Figure 2.
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gkr1235-F3: Comparative analysis Win motif binding modes. (A) Superimposition of WDR5-bound MLL1 (beige) and MLL2 (yellow) peptides. (B) Overlay of MLL1 (beige) and MLL4 (green) peptides in complex with WDR5 (grey). (C) Structural alignment of WDR5–MLL1Win and WDR5–SET1AWin complex in which carbons of the peptides are highlighted as in Figure 2. Residues of WDR5 peptidyl-arginine-binding adopting divergent conformation between the complexes are rendered as pink carbon atoms. Hydrogen bonds and water molecules are rendered as in Figure 2.

Mentions: Despite high sequence homology and analogous binding modes of the P−3, P−2, P−1 and P0 residues, structural alignment of the WDR5–Win complexes reveals notable structural differences. In comparison with MLL1Win, the backbone of the MLL2Win and MLL4Win P−3 residue is rotate 180°, which results in additional water-mediated and direct hydrogen bonds with WDR5 (Figure 3). This rotation leads to a small structural displacement of the P−2 backbone with negligible consequences on the positioning of C5063 (MLL2), S4708 (MLL3), A2509 (MLL4), S1493 (SET1A) and C1883 (SET1B) side chains and their interactions with WDR5. However, in clear contrast to the P−2, P−1, P0, P+1 and P+2 residues, the P+3 to P+5 residues adopt divergent orientations. MLL2Win and MLL3Win peptides, which bind analogously to WDR5, interact in such a way that their respective C-termini point towards blade 5 of WDR5 while MLL4Win and MLL1Win adopt a conformation placing their C-terminal ends towards blade 4 of the β-propeller. SET1AWin and SET1BWin peptides bind in an intermediate orientation such that their C-termini are maintained on the surface of blades 4 and 5 of WDR5 (Figure 2A). Given the structural differences adopted by residues succeeding the P+2 residue (Figure 3), we purported that each peptide would engage in distinct interactions with WDR5. The backbone of P+3 Y2514 of MLL4Win, which binds similarly to H3769 of MLL1Win, forms direct and water-mediated hydrogen bonds with Asp-172 and Lys-259 carboxylate and carbonyl groups, respectively. In addition, its aromatic ring makes hydrophobic contacts with the side chains of Tyr-191, Pro-173 and Phe-149. In contrast to the solvent exposed P+4 L2516, the P+5 R2517 side chain is nestled in a small cleft formed by the surface of blade 4 and the loop connecting blades 4 and 5 of WDR5 (Figure 3B). This crevice, which is composed of Tyr-191, Asp-192, Gly-193, Asn-214, Pro-215 and Pro-216, likely orients the R2517 side chain in a permissive orientation to engage in direct hydrogen bonds with the backbone carbonyl groups of Tyr-191 and Asn-214 and van der Waals contacts with Pro-216.Figure 2.


The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases.

Zhang P, Lee H, Brunzelle JS, Couture JF - Nucleic Acids Res. (2012)

Comparative analysis Win motif binding modes. (A) Superimposition of WDR5-bound MLL1 (beige) and MLL2 (yellow) peptides. (B) Overlay of MLL1 (beige) and MLL4 (green) peptides in complex with WDR5 (grey). (C) Structural alignment of WDR5–MLL1Win and WDR5–SET1AWin complex in which carbons of the peptides are highlighted as in Figure 2. Residues of WDR5 peptidyl-arginine-binding adopting divergent conformation between the complexes are rendered as pink carbon atoms. Hydrogen bonds and water molecules are rendered as in Figure 2.
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Related In: Results  -  Collection

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gkr1235-F3: Comparative analysis Win motif binding modes. (A) Superimposition of WDR5-bound MLL1 (beige) and MLL2 (yellow) peptides. (B) Overlay of MLL1 (beige) and MLL4 (green) peptides in complex with WDR5 (grey). (C) Structural alignment of WDR5–MLL1Win and WDR5–SET1AWin complex in which carbons of the peptides are highlighted as in Figure 2. Residues of WDR5 peptidyl-arginine-binding adopting divergent conformation between the complexes are rendered as pink carbon atoms. Hydrogen bonds and water molecules are rendered as in Figure 2.
Mentions: Despite high sequence homology and analogous binding modes of the P−3, P−2, P−1 and P0 residues, structural alignment of the WDR5–Win complexes reveals notable structural differences. In comparison with MLL1Win, the backbone of the MLL2Win and MLL4Win P−3 residue is rotate 180°, which results in additional water-mediated and direct hydrogen bonds with WDR5 (Figure 3). This rotation leads to a small structural displacement of the P−2 backbone with negligible consequences on the positioning of C5063 (MLL2), S4708 (MLL3), A2509 (MLL4), S1493 (SET1A) and C1883 (SET1B) side chains and their interactions with WDR5. However, in clear contrast to the P−2, P−1, P0, P+1 and P+2 residues, the P+3 to P+5 residues adopt divergent orientations. MLL2Win and MLL3Win peptides, which bind analogously to WDR5, interact in such a way that their respective C-termini point towards blade 5 of WDR5 while MLL4Win and MLL1Win adopt a conformation placing their C-terminal ends towards blade 4 of the β-propeller. SET1AWin and SET1BWin peptides bind in an intermediate orientation such that their C-termini are maintained on the surface of blades 4 and 5 of WDR5 (Figure 2A). Given the structural differences adopted by residues succeeding the P+2 residue (Figure 3), we purported that each peptide would engage in distinct interactions with WDR5. The backbone of P+3 Y2514 of MLL4Win, which binds similarly to H3769 of MLL1Win, forms direct and water-mediated hydrogen bonds with Asp-172 and Lys-259 carboxylate and carbonyl groups, respectively. In addition, its aromatic ring makes hydrophobic contacts with the side chains of Tyr-191, Pro-173 and Phe-149. In contrast to the solvent exposed P+4 L2516, the P+5 R2517 side chain is nestled in a small cleft formed by the surface of blade 4 and the loop connecting blades 4 and 5 of WDR5 (Figure 3B). This crevice, which is composed of Tyr-191, Asp-192, Gly-193, Asn-214, Pro-215 and Pro-216, likely orients the R2517 side chain in a permissive orientation to engage in direct hydrogen bonds with the backbone carbonyl groups of Tyr-191 and Asn-214 and van der Waals contacts with Pro-216.Figure 2.

Bottom Line: We herein provide biochemical and structural evidence showing that WDR5 binds the Win motifs of MLL2-4, SET1A and SET1B.Comparative analysis of WDR5-Win complexes reveals that binding of the Win motifs is achieved by the plasticity of WDR5 peptidyl-arginine-binding cleft allowing the C-terminal ends of the Win motifs to be maintained in structurally divergent conformations.Overall, our findings illustrate the function of WDR5 in scaffolding the SET1 family of KMTs and further emphasize on the important role of WDR5 in regulating global histone H3 Lys-4 methylation.

View Article: PubMed Central - PubMed

Affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.

ABSTRACT
In mammals, the SET1 family of lysine methyltransferases (KMTs), which includes MLL1-5, SET1A and SET1B, catalyzes the methylation of lysine-4 (Lys-4) on histone H3. Recent reports have demonstrated that a three-subunit complex composed of WD-repeat protein-5 (WDR5), retinoblastoma-binding protein-5 (RbBP5) and absent, small, homeotic disks-2-like (ASH2L) stimulates the methyltransferase activity of MLL1. On the basis of studies showing that this stimulation is in part controlled by an interaction between WDR5 and a small region located in close proximity of the MLL1 catalytic domain [referred to as the WDR5-interacting motif (Win)], it has been suggested that WDR5 might play an analogous role in scaffolding the other SET1 complexes. We herein provide biochemical and structural evidence showing that WDR5 binds the Win motifs of MLL2-4, SET1A and SET1B. Comparative analysis of WDR5-Win complexes reveals that binding of the Win motifs is achieved by the plasticity of WDR5 peptidyl-arginine-binding cleft allowing the C-terminal ends of the Win motifs to be maintained in structurally divergent conformations. Consistently, enzymatic assays reveal that WDR5 plays an important role in the optimal stimulation of MLL2-4, SET1A and SET1B methyltransferase activity by the RbBP5-ASH2L heterodimer. Overall, our findings illustrate the function of WDR5 in scaffolding the SET1 family of KMTs and further emphasize on the important role of WDR5 in regulating global histone H3 Lys-4 methylation.

Show MeSH