ISDA

Entry Detail

PDB ID:

6PZV

Keywords:

DNA BINDING PROTEIN

Title:

Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin

Biological Source:

Source Organism:

Homo sapiens, Bos taurus

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2019-08-01

Release Date:

2020-07-15

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.01 Å

R-Value Free:

0.27

R-Value Work:

0.21

R-Value Observed:

0.22

Space Group:

P 21 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Ubiquitin
Chain IDs:A, B, E, F
Chain Length:77
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P0CG47 Pfam ID:PF00240

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA (cytosine-5)-methyltransferase 1
Chain IDs:C, G
Chain Length:247
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:Q24K09 Pfam ID:PF12047

Protein Blast

Polymer Type:polypeptide(L)
Description:Histone H3.3
Chain IDs:D, H
Chain Length:26
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P84243

Modified Residue

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

Ligand Molecules

FLC

Primary Citation

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation.

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

Proc.Natl.Acad.Sci.USA 117 18439 18447 (2020)

PMID: 32675241 DOI: 10.1073/pnas.2009316117

Abstact

In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.

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Primary Citation of related structures