ISDA

Entry Detail

PDB ID:

7XIB

EMDB ID:

EMD-33201

Keywords:

TRANSFERASE/DNA

Title:

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)

Biological Source:

Source Organism:

Homo sapiens, synthetic construct

Host Organism:

Baculovirus expression vector pFastBac1-HM

PDB Version:

Deposition Date:

2022-04-12

Release Date:

2022-11-30

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.23 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA (cytosine-5)-methyltransferase 1
Chain IDs:A
Chain Length:1266
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P26358 Pfam ID:PF12047, PF02008, PF01426, PF00145 EC:2.1.1.37

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
Chain IDs:B
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3')
Chain IDs:C
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

Structural basis for activation of DNMT1.

Kikuchi, A, Onoda, H, Yamaguchi, K, Kori, S, Matsuzawa, S, Chiba, Y, Tanimoto, S, Yoshimi, S, Sato, H, Yamagata, A, Shirouzu, M, Adachi, N, Sharif, J, Koseki, H, Nishiyama, A, Nakanishi, M, Defossez, P.A, Arita, K.Show

Nat Commun 13 7130 7130 (2022)

PMID: 36414620 DOI: 10.1038/s41467-022-34779-4

Abstact

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.

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