ISDA

Entry Detail

PDB ID:

7LMK

Keywords:

TRANSFERASE

Title:

Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3

Biological Source:

Source Organism:

Bos taurus, Homo sapiens

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2021-02-05

Release Date:

2021-02-17

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.65 Å

R-Value Free:

0.25

R-Value Work:

0.20

R-Value Observed:

0.21

Space Group:

P 2 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA (cytosine-5)-methyltransferase 1
Chain IDs:A, B, C, D
Chain Length:158
Number of Molecules:4
Biological Source:Bos taurus

UniProt ID:Q24K09 Pfam ID:PF01426

Protein Blast

Polymer Type:polypeptide(L)
Description:Histone H4
Chain IDs:E (auth: F), F (auth: G), G (auth: H), H (auth: I)
Chain Length:13
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62805

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
M3L	E	LYS	modified residue

Ligand Molecules

Primary Citation

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation.

Ren, W, Fan, H, Grimm, S.A, Kim, J.J, Li, L, Guo, Y, Petell, C.J, Tan, X.F, Zhang, Z.M, Coan, J.P, Yin, J, Kim, D.I, Gao, L, Cai, L, Khudaverdyan, N, Cetin, B, Patel, D.J, Wang, Y, Cui, Q, Strahl, B.D, Gozani, O, Miller, K.M, O'Leary, S.E, Wade, P.A, Wang, G.G, Song, J.Show

Nat Commun 12 2490 2490 (2021)

PMID: 33941775 DOI: 10.1038/s41467-021-22665-4

Abstact

DNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically 'recognizes' H4K20me3 via its first bromo-adjacent-homology domain (DNMT1BAH1). Engagement of DNMT1BAH1-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1's activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability.

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Primary Citation of related structures