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

Zhang, Pamela; Lee, Hwabin; Brunzelle, J.S.; Couture, Jean

doi:10.1093/nar/gkr1235

Cited by 105 publications

(158 citation statements)

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“…While each of these multisubunit protein complexes contains unique subunits, each member of the KMT2 family associates with a common set of four evolutionarily conserved regulatory proteins; namely, WDR5, RbBP5, Ash2L, and DPY30 (WRAD) (Couture and Skiniotis 2013). The foursubunit complex directly binds the SET domain of KMT2 enzymes and serves as an essential modulatory platform stimulating the enzymatic activity of each member within this family (Dou et al 2006;Steward et al 2006;Patel et al 2009;Avdic et al 2011;Zhang et al 2012).In an attempt to understand the structural mechanisms underlying the assembly of the WRAD complex and stimulation of MLL1 methyltransferase activity, several studies have dissected the structure and function of each WRAD subunit (Couture and Skiniotis 2013). WDR5 is crucial for the structural integrity of the complex and acts as a bridge linking each member of the KMT2 family (Dharmarajan et al 2012;Zhang et al 2012) to the regulatory subunits RbBP5, Ash2L, and DPY-30 (Odho et al 2010;Avdic et al 2011).…”

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A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation

et al. 2015

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The methyltransferase activity of the trithorax group (TrxG) protein MLL1 found within its COMPASS (complex associated with SET1)-like complex is allosterically regulated by a four-subunit complex composed of WDR5, RbBP5, Ash2L, and DPY30 (also referred to as WRAD). We report structural evidence showing that in WRAD, a concave surface of the Ash2L SPIa and ryanodine receptor (SPRY) domain binds to a cluster of acidic residues, referred to as the D/E box, in RbBP5. Mutational analysis shows that residues forming the Ash2L/RbBP5 interface are important for heterodimer formation, stimulation of MLL1 catalytic activity, and erythroid cell terminal differentiation. We also demonstrate that a phosphorylation switch on RbBP5 stimulates WRAD complex formation and significantly increases KMT2 (lysine [K] methyltransferase 2) enzyme methylation rates. Overall, our findings provide structural insights into the assembly of the WRAD complex and point to a novel regulatory mechanism controlling the activity of the KMT2/COMPASS family of lysine methyltransferases.Supplemental material is available for this article.Received October 27, 2014; revised version accepted December 15, 2014. The methyltransferase activity of the trithorax group (TrxG) protein MLL1 as well as the other members of the KMT2 (lysine [K] methyltransferase 2) family found within COMPASS (complex associated with SET1) catalyzes the site-specific methylation of the e-amine of Lys4 (K4) of histone H3 (Shilatifard 2012). While these enzymes share the ability to methylate the same residue on histone H3, the catalytic activity of these enzymes is linked to different biological processes. MLL1/MLL2 di/trimethylate H3K4 (H3K4me2/3) and regulate Hox gene expression during embryonic development (Yu et al. 1995;Dou et al. 2006). MLL3/MLL4 regulate adipogenesis ) and primarily monomethylate H3K4 (H3K4me1) at both enhancer (Herz et al. 2012;Hu et al. 2013) and promoter (Cheng et al. 2014) regions, while SET1A/B are the primary H3K4 trimethyltransferases (Wu et al. 2008). However, despite divergence in catalytic activity and functional roles, enzymes of the KMT2/COMPASS family must assemble into multisubunit complexes to carry out their biological functions.Our molecular understanding of the protein complexes involved in H3K4 methylation stems from the isolation of COMPASS from Saccharomyces cerevisiae (Miller et al. 2001;Roguev et al. 2001;Krogan et al. 2002;Dehe et al. 2006). These studies demonstrated that regulatory subunits found within COMPASS and mammalian COMPASS-like complexes play key roles in stabilizing the enzyme and stimulating its methyltransferase activity as well as targeting the protein complex to specific genomic loci (Couture and Skiniotis 2013). While each of these multisubunit protein complexes contains unique subunits, each member of the KMT2 family associates with a common set of four evolutionarily conserved regulatory proteins; namely, WDR5, RbBP5, Ash2L, and DPY30 (WRAD) (Couture and Skiniotis 2013). The foursubunit complex directly binds ...

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A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation

et al. 2015

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“…13 Although there is significant divergence in the amino acid sequences of WIN motifs close to the critical arginine residue, the plasticity of the WDR5 arginine binding pocket allows such an interaction with the WIN motifs of all MLLs. 13 MLLs have been reported to be essential for embryonic development and biological processes 14−17 and have been widely implicated in a variety of cancers. 18−22 As almost all MLLs show minimal or no activity in the absence of the complex components (WDR5 in particular), 13 identifying WDR5−MLL interaction antagonists has been proposed as a potentially selective alternative to active site directed inhibitors of MLL methyltransferase activity.…”

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“…Subsequent displacement of the fluorine from this common intermediate using a variety of secondary amines gave rise to the substituted benzamides 2 and 5−18 in high overall yields. In several cases (13,15,17), an additional step involving Boc deprotection was required.…”

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Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction

Bolshan

Getlik

Kuznetsova

et al. 2013

ACS Med. Chem. Lett.

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The WD40-repeat protein WDR5 plays a critical role in maintaining the integrity of MLL complexes and fully activating their methyltransferase function. MLL complexes, the trithorax-like family of SET1 methyltransferases, catalyze trimethylation of lysine 4 on histone 3, and they have been widely implicated in various cancers. Antagonism of WDR5 and MLL subunit interaction by small molecules has recently been presented as a practical way to inhibit activity of the MLL1 complex, and N-(2-(4-methylpiperazin-1-yl)-5-substituted-phenyl) benzamides were reported as potent and selective antagonists of such an interaction. Here, we describe the protein crystal structure guided optimization of prototypic compound 2 (K dis = 7 μM), leading to identification of more potent antagonist 47 (K dis = 0.3 μM). KEYWORDS: WDR5, MLL, SET1 methyltransferase complex, peptide binding site, small molecule antagonists T he SET1-family of human histone methyltransferases (SET1A, SET1B, MLL1, MLL2, MLL3, and MLL4) contribute to active chromatin via mono-, di-, and trimethylation of lysine 4 on histone H3. 1−3 MLLs are S-adenosyl methionine (SAM) dependent lysine methyltransferases that work optimally when in complex with other components; WDR5 (WD40 repeat protein 5), RbBP5 (retinoblastomabinding protein-5), ASH2L (absent small homeotic disks-2-like), and DPY-30 (WRAD). 4 WDR5 has been shown to be essential for complex integrity and for fully activating MLL methyltransferase function. 5−7 In the peptide-bound structure, WDR5 adopts a donutshaped WD40-repeat fold with a deep central cavity that normally accommodates an arginine side chain of interacting peptides. 8 WDR5 binds to the "WDR5 INteracting" (WIN) motif of MLL1 through the peptidyl arginine-binding cleft. 8−12 A crystal structure of WDR5 in complex with MLL1 WIN peptide revealed the critical role of arginine 3765 of MLL1 in complex formation. 9 A similar interaction has been reported for WDR5 and the WIN region of all SET1 family lysine methyltransferases, with reported K D values of 1.13, 0.16, 2.03, 0.03, 0.26, and 0.10 μM for MLL1-4, SET1A, and SET1B WIN peptides, respectively. 13 Although there is significant divergence in the amino acid sequences of WIN motifs close to the critical arginine residue, the plasticity of the WDR5 arginine binding pocket allows such an interaction with the WIN motifs of all MLLs. 13 MLLs have been reported to be essential for embryonic development and biological processes 14−17 and have been widely implicated in a variety of cancers. 18−22 As almost all MLLs show minimal or no activity in the absence of the complex components (WDR5 in particular), 13 identifying WDR5−MLL interaction antagonists has been proposed as a potentially selective alternative to active site directed inhibitors of MLL methyltransferase activity. Such antagonists could serve as a starting point for the development of potential therapeutics to treat MLL-rearranged leukemias or other related cancers. 23 Recent reports detailing the use of short arginine contain...

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“…1A). 44,45 Additional structural studies revealed that WDR5 binds RbBP5 via a V-shaped cleft located on the opposite side of the arginine binding cleft. 39,40 The same studies also demonstrated that a valine-aspartate-valine (VDV) motif of RbBP5 is necessary for binding to WDR5.…”

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confidence: 99%

Assembling a COMPASS

Couture

Skiniotis

2013

Epigenetics

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P ost-translational modifications ofhistone proteins lie at the heart of the epigenetic landscape in the cell's nucleus and the precise regulation of gene expression. A myriad of studies have showed that several histone-modifying enzymes are controlled by modulatory protein partner subunits and other post-transcriptional modifications deposited in the vicinity of the targeted site. All together, these mechanisms create an intricate network of interactions that regulate enzymatic activities and ultimately control the site-specific deposition of covalent modifications. In this Point-of-View, we discuss our evolving understanding on the assembly and architecture of histone H3 Lys-4 (H3K4) methyltransferase COMPASS complexes and the techniques that progressively allowed us to better define the molecular basis of complex formation and function. We further briefly discuss some of the challenges lying ahead and additional approaches required to understand mechanistic details for the function of such complexes.

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

Cited by 105 publications

References 49 publications

A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation

A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation

Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction

Assembling a COMPASS

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