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Structure paper

TitleStructural basis for activation of DNMT1.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 7130, Year 2022
Publish dateNov 21, 2022
AuthorsAmika Kikuchi / Hiroki Onoda / Kosuke Yamaguchi / Satomi Kori / Shun Matsuzawa / Yoshie Chiba / Shota Tanimoto / Sae Yoshimi / Hiroki Sato / Atsushi Yamagata / Mikako Shirouzu / Naruhiko Adachi / Jafar Sharif / Haruhiko Koseki / Atsuya Nishiyama / Makoto Nakanishi / Pierre-Antoine Defossez / Kyohei Arita /
PubMed AbstractDNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human ...DNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human DNMT1 bound to its two natural activators: hemimethylated DNA and ubiquitinated histone H3. We find that a hitherto unstudied linker, between the RFTS and CXXC domains, plays a key role for activation. It contains a conserved α-helix which engages a crucial "Toggle" pocket, displacing a previously described inhibitory linker, and allowing the DNA Recognition Helix to spring into the active conformation. This is accompanied by large-scale reorganization of the inhibitory RFTS and CXXC domains, allowing the enzyme to gain full activity. Our results therefore provide a mechanistic basis for the activation of DNMT1, with consequences for basic research and drug design.
External linksNat Commun / PubMed:36414620 / PubMed Central
MethodsEM (single particle)
Resolution2.23 - 3.52 Å
Structure data

33200

7xi9

EMDB-33200, PDB-7xi9:
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)
Method: EM (single particle) / Resolution: 2.52 Å

33201

7xib

EMDB-33201, PDB-7xib:
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)
Method: EM (single particle) / Resolution: 2.23 Å

EMDB-33298: Cryo-EM map of apo-DNMT1 (aa:351-1616)
Method: EM (single particle) / Resolution: 3.52 Å

EMDB-33299: Cryo-EM map of DNMT1 (aa:351-1616) in complex with ubiquitinated H3
Method: EM (single particle) / Resolution: 3.45 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSFERASE/DNA / DNA methyltransferase / TRANSFERASE-DNA COMPLEX

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