Protein Structure and Folding
The Methyltransferase NSD3 Has Chromatin-binding Motifs, PHD5-C5HCH, That Are Distinct from Other NSD (Nuclear Receptor SET Domain) Family Members in Their Histone H3 Recognition*

https://doi.org/10.1074/jbc.M112.426148Get rights and content
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The NSD (nuclear receptor SET domain-containing) family members, consisting of NSD1, NSD2 (MMSET/WHSC1), and NSD3 (WHSC1L1), are SET domain-containing methyltransferases and aberrant expression of each member has been implicated in multiple diseases. They have specific mono- and dimethylase activities for H3K36, whereas play nonredundant roles during development. Aside from the well characterized catalytic SET domain, NSD proteins have multiple potential chromatin-binding motifs that are clinically relevant, including the fifth plant homeodomain (PHD5) and the adjacent Cys-His-rich domain (C5HCH) located at the C terminus. Herein, we report the crystal structures of the PHD5-C5HCH module of NSD3, in the free state and in complex with H31–7 (H3 residues 1–7), H31–15 (H3 residues 1–15), and H31–15K9me3 (H3 residues 1–15 with trimethylation on K9) peptides. These structures reveal that the PHD5 and C5HCH domains fold into a novel integrated PHD-PHD-like structural module with H3 peptide bound only on the surface of PHD5 and provide the molecular basis for the recognition of unmodified H3K4 and trimethylated H3K9 by NSD3 PHD5. Structural studies and binding assays show that differences exist in histone binding specificity of the PHD5 domain between three members of the NSD family. For NSD2, the PHD5-C5HCH:H3 N terminus interaction is largely conserved, although with a stronger preference for unmethylated H3K9 (H3K9me0) than trimethylated H3K9 (H3K9me3), and NSD1 PHD5-C5HCH does not bind to H3 peptides. Our results shed light on how NSD proteins that mediate H3K36 methylation are localized to specific genomic sites and provide implications for the mechanism of functional diversity of NSD proteins.

Background: NSD proteins are histone H3K36 methyltransferases linked to multiple human diseases.

Results: Crystal structures of chromatin-binding motifs, PHD5-C5HCH, of NSD3 bound to the H3 N-terminal peptide were solved.

Conclusion: PHD5-C5HCHs of the NSD family are conserved in their overall structure yet variant in H3 recognition.

Significance: Their variant recognitions may play a role in the localization of NSD proteins to different genomic sites.

Chromatin Histone Modification
Crystal Structure
Epigenetics
Histone Methylation
NMR
H3K36
H3K4
NSD Family
PHD Finger
WHSC1

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The atomic coordinates and structure factors (codes 4GND, 4GNE, 4GNF, and 4GNG) have been deposited in the Protein Data Bank (http://wwpdb.org/).

The resonance assignments of PHD5-C5HCHNSD3 have been deposited in the Biological Magnetic Resonance Data Bank (BMRB) under accession numbers 18664.

*

This work was supported by National Basic Research Program of China 973 Program Grants 2011CB966302, 2012CB917201, and 2011CB911104 and Chinese National Natural Science Foundation Grants 30830031 and 31170693.

This article contains supplemental Tables S1 and S2 and Figs. S1–S16.

1

Both authors contributed equally to this work.