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TitleStructural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance.
Journal, issue, pagesMol Cell, Vol. 82, Issue 6, Page 1186-11198.e6, Year 2022
Publish dateMar 17, 2022
AuthorsJuncheng Wang / Sandra Catania / Chongyuan Wang / M Jason de la Cruz / Beiduo Rao / Hiten D Madhani / Dinshaw J Patel /
PubMed AbstractEpigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance type cytosine methyltransferase identified in the fungal or protist ...Epigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance type cytosine methyltransferase identified in the fungal or protist kingdoms, the first dependent on adenosine triphosphate (ATP), and the most hemimethyl-DNA-specific enzyme known. To understand these novel properties, we solved cryo-EM structures of CnDNMT5 in three states. These studies reveal an elaborate allosteric cascade in which hemimethylated DNA binding first activates the SNF2 ATPase domain by a large rigid body rotation while the target cytosine partially flips out of the DNA duplex. ATP binding then triggers striking structural reconfigurations of the methyltransferase catalytic pocket to enable cofactor binding, completion of base flipping, and catalysis. Bound unmethylated DNA does not open the catalytic pocket and is instead ejected upon ATP binding, driving high fidelity. This unprecedented chaperone-like, enzyme-remodeling role of the SNF2 ATPase domain illuminates how energy is used to enable faithful epigenetic memory.
External linksMol Cell / PubMed:35202575 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.8 Å
Structure data

24292

7r76

EMDB-24292, PDB-7r76:
Cryo-EM structure of DNMT5 in apo state
Method: EM (single particle) / Resolution: 3.2 Å

24294

7r77

EMDB-24294, PDB-7r77:
Cryo-EM structure of DNMT5 binary complex with hemimethylated DNA
Method: EM (single particle) / Resolution: 3.0 Å

24295

7r78

EMDB-24295: Cryo-EM structure of DNMT5 quaternary complex with hemimethylated DNA, AMP-PNP and SAH
PDB-7r78: cryo-EM structure of DNMT5 quaternary complex with hemimethylated DNA, AMP-PNP and SAH
Method: EM (single particle) / Resolution: 3.5 Å

25577

7t02

EMDB-25577, PDB-7t02:
Cryo-EM structure of DNMT5 pseudo-ternary complex solved by incubation with hemimethylated DNA and SAM
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • cryptococcus neoformans (fungus)
  • cryptococcus neoformans var. grubii serotype a (strain h99 / atcc 208821 / cbs 10515 / fgsc 9487) (fungus)
  • cryptococcus neoformans var. grubii h99 (fungus)
KeywordsTRANSFERASE / Cytosine-5 methyltransferase / SNF2 ATPase / TRANSFERASE/DNA / hemimethylated DNA / TRANSFERASE-DNA complex / ATP / SAM

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