5.1 Recognition of the Histone H3 Tail by WDR5
The plasticity of WD40 β-propeller recognition sites is an important and recurring
feature in binding studies, and this is underlined in the investigation of WDR5 and
its interaction with histone H3. This β-propeller protein is a member a multiprotein
complex that is associated with the KMT2 methyltransferase family [205, 206]. The
KMT2s are a family of six histone H3K4-specific methyltransferases, KMT2A-D,
KMT2F, and KMT2G, also known as mixed-lineage leukemia protein 1–4 (MLL1–
MLL4) and SET domain-containing protein 1A and 1B (SETD1A and SETD1B),
respectively. These enzymes are implicated in the positive transcriptional regulation
of critical developmental genes [207]. Although the conserved C-terminal catalytic
SET domain consists of only 150 amino acids, the KMT2s are large multidomain
proteins. It is presumed that the majority of the protein domains are involved in
ensuring a highly specific and regulated gene targeting. However, the KMT2
SET domain is not competent for methyl transfer on its own but requires assembly
into a multiprotein complex for full biochemical activity [205, 206]. This associated
“core complex” consists of four proteins, ASH2L ([absent, small, or homeotic]like protein), DPY30, and two WD40 β-propeller proteins, WDR5 and RBBP5.
Both knockdown experiments in cells and in vitro reconstitution experiments confirm that assembly of the full complex is required for full SET domain activation
[205, 208, 209]. Early biochemical studies indicated that WDR5 might function in
histone H3 amino tail recognition and recruitment of the complex to the nucleosome
and even suggested that WDR5 may sense the H3K4 methylation state [209].
However, subsequently, structural analyses revealed that the β-propeller robustly
recognized only a short sequence motif (Ala-Arg-Thr) in the amino tail of histone
H3 [210]. The H3-binding site is located in the axial region on the top of the WDR5
propeller [210].
The integral role that the histone H3R2 side chain has in the histone recognition
mechanism of the WDR5 β-propeller is particularly significant because this residue
is itself a target for posttranslational modifications associated with epigenetic regulation. The R2 arginine side chain can be asymmetrically dimethylated (H3R2me2a)
by PRMT6 or symmetrically dimethylated (H3R2me2s) by PRMT5 and PRMT7
[202, 203]. The effect that these two types of arginine methyl modification have
on binding to WDR5 is surprisingly divergent. Whereas the H3R2me2a modification
effectively ablates binding to WDR5, in contrast, the H3R2me2s modification
results in up to tenfold higher binding affinity [202, 203, 210]. WDR5 is rather
an arginine reader than a methyllysine reader. This is even more underlined by
the observation that WDR5 binds several arginine-containing peptides, with some
of them even lacking a lysine residue (e.g., SET1A, SET1B, and MLL1–MLL4).
Aside from the arginine side chain itself, the interaction with H3 does not include
sequence-specific contacts. In crystallization studies, the plasticity of the site has
been highlighted by its occupation by a range of peptide sequences. These included
the amino terminus of a neighboring WDR5 molecule in the lattice (sequence ARA),
or part of the purification tag (GRE) [211]. The role of WDR5 in the cell is not
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373
The plasticity of WD40 β-propeller recognition sites is an important and recurring
feature in binding studies, and this is underlined in the investigation of WDR5 and
its interaction with histone H3. This β-propeller protein is a member a multiprotein
complex that is associated with the KMT2 methyltransferase family [205, 206]. The
KMT2s are a family of six histone H3K4-specific methyltransferases, KMT2A-D,
KMT2F, and KMT2G, also known as mixed-lineage leukemia protein 1–4 (MLL1–
MLL4) and SET domain-containing protein 1A and 1B (SETD1A and SETD1B),
respectively. These enzymes are implicated in the positive transcriptional regulation
of critical developmental genes [207]. Although the conserved C-terminal catalytic
SET domain consists of only 150 amino acids, the KMT2s are large multidomain
proteins. It is presumed that the majority of the protein domains are involved in
ensuring a highly specific and regulated gene targeting. However, the KMT2
SET domain is not competent for methyl transfer on its own but requires assembly
into a multiprotein complex for full biochemical activity [205, 206]. This associated
“core complex” consists of four proteins, ASH2L ([absent, small, or homeotic]like protein), DPY30, and two WD40 β-propeller proteins, WDR5 and RBBP5.
Both knockdown experiments in cells and in vitro reconstitution experiments confirm that assembly of the full complex is required for full SET domain activation
[205, 208, 209]. Early biochemical studies indicated that WDR5 might function in
histone H3 amino tail recognition and recruitment of the complex to the nucleosome
and even suggested that WDR5 may sense the H3K4 methylation state [209].
However, subsequently, structural analyses revealed that the β-propeller robustly
recognized only a short sequence motif (Ala-Arg-Thr) in the amino tail of histone
H3 [210]. The H3-binding site is located in the axial region on the top of the WDR5
propeller [210].
The integral role that the histone H3R2 side chain has in the histone recognition
mechanism of the WDR5 β-propeller is particularly significant because this residue
is itself a target for posttranslational modifications associated with epigenetic regulation. The R2 arginine side chain can be asymmetrically dimethylated (H3R2me2a)
by PRMT6 or symmetrically dimethylated (H3R2me2s) by PRMT5 and PRMT7
[202, 203]. The effect that these two types of arginine methyl modification have
on binding to WDR5 is surprisingly divergent. Whereas the H3R2me2a modification
effectively ablates binding to WDR5, in contrast, the H3R2me2s modification
results in up to tenfold higher binding affinity [202, 203, 210]. WDR5 is rather
an arginine reader than a methyllysine reader. This is even more underlined by
the observation that WDR5 binds several arginine-containing peptides, with some
of them even lacking a lysine residue (e.g., SET1A, SET1B, and MLL1–MLL4).
Aside from the arginine side chain itself, the interaction with H3 does not include
sequence-specific contacts. In crystallization studies, the plasticity of the site has
been highlighted by its occupation by a range of peptide sequences. These included
the amino terminus of a neighboring WDR5 molecule in the lattice (sequence ARA),
or part of the purification tag (GRE) [211]. The role of WDR5 in the cell is not
Methyl-Readers and Inhibitors
373