7LMM

Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2

  • Classification: TRANSFERASE
  • Organism(s): Bos taurus, Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-02-05 Released: 2021-02-17 
  • Deposition Author(s): Ren, W., Song, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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.

(2021) Nat Commun 12: 2490-2490

  • DOI: https://doi.org/10.1038/s41467-021-22665-4
  • Primary Citation of Related Structures:  
    7LMK, 7LMM

  • PubMed Abstract: 

    • 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 ...

    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 (DNMT1 BAH1 ). Engagement of DNMT1 BAH1 -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.

    Organizational Affiliation: 

    Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA. jikui.song@ucr.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1A, B, C, D158Bos taurusMutation(s): 0 
Gene Names: DNMT1
EC: 2.1.1.37
UniProt
Find proteins for Q24K09 (Bos taurus)
Explore Q24K09 
Go to UniProtKB:  Q24K09
Entity Groups  
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UniProt GroupQ24K09
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4E [auth F],
F [auth G],
G [auth I],
H		13Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY		E [auth F],
F [auth G],
G [auth I],
H		L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.696α = 90
b = 80.281β = 90
c = 130.424γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM119721

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references