Molecular Cell
Volume 79, Issue 1, 2 July 2020, Pages 127-139.e4
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Article
ATP Hydrolysis by the SNF2 Domain of Dnmt5 Is Coupled to Both Specific Recognition and Modification of Hemimethylated DNA

https://doi.org/10.1016/j.molcel.2020.04.029Get rights and content
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Highlights

  • Maintenance DNA methylation by Dnmt5 requires ATP hydrolysis by its SNF2 domain

  • Hemimethylated DNA substrates preferentially stimulate Dnmt5 ATPase

  • Mutation of Dnmt5 SNF2 domain decouples ATPase from DNA methyltransferase activity

  • Stabilization of active DNMT domain conformation stimulates SNF2 ATPase

Summary

C.neoformans Dnmt5 is an unusually specific maintenance-type CpG methyltransferase (DNMT) that mediates long-term epigenome evolution. It harbors a DNMT domain and SNF2 ATPase domain. We find that the SNF2 domain couples substrate specificity to an ATPase step essential for DNA methylation. Coupling occurs independent of nucleosomes. Hemimethylated DNA preferentially stimulates ATPase activity, and mutating Dnmt5’s ATP-binding pocket disproportionately reduces ATPase stimulation by hemimethylated versus unmethylated substrates. Engineered DNA substrates that stabilize a reaction intermediate by mimicking a “flipped-out” conformation of the target cytosine bypass the SNF2 domain’s requirement for hemimethylation. This result implies that ATP hydrolysis by the SNF2 domain is coupled to the DNMT domain conformational changes induced by preferred substrates. These findings establish a new role for a SNF2 ATPase: controlling an adjoined enzymatic domain’s substrate recognition and catalysis. We speculate that this coupling contributes to the exquisite specificity of Dnmt5 via mechanisms related to kinetic proofreading.

Keywords

DNA methylation
DNA methyltransferase
ATPase
epigenetics
Dnmt5
enzyme mechanism
enzyme specificity
maintenance methylation
SNF2

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