6W8D

Structure of DNMT3A (R882H) in complex with CGT DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Literature

Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.

Anteneh, H., Fang, J., Song, J.

(2020) Nat Commun 11: 2294-2294

  • DOI: https://doi.org/10.1038/s41467-020-16213-9
  • Primary Citation of Related Structures:  
    6W89, 6W8B, 6W8D, 6W8J

  • PubMed Abstract: 

    • DNA methyltransferase DNMT3A is essential for establishment of mammalian DNA methylation during development. The R882H DNMT3A is a hotspot mutation in acute myeloid leukemia (AML) causing aberrant DNA methylation. However, how this mutation affects the structure and function of DNMT3A remains unclear ...

    DNA methyltransferase DNMT3A is essential for establishment of mammalian DNA methylation during development. The R882H DNMT3A is a hotspot mutation in acute myeloid leukemia (AML) causing aberrant DNA methylation. However, how this mutation affects the structure and function of DNMT3A remains unclear. Here we report structural characterization of wild-type and R882H-mutated DNMT3A in complex with DNA substrates with different sequence contexts. A loop from the target recognition domain (TRD loop) recognizes the CpG dinucleotides in a +1 flanking site-dependent manner. The R882H mutation reduces the DNA binding at the homodimeric interface, as well as the molecular link between the homodimeric interface and TRD loop, leading to enhanced dynamics of TRD loop. Consistently, in vitro methylation analyses indicate that the R882H mutation compromises the enzymatic activity, CpG specificity and flanking sequence preference of DNMT3A. Together, this study uncovers multiple defects of DNMT3A caused by the R882H mutation in AML.

    Organizational Affiliation: 

    Department of Biochemistry, University of California, Riverside, CA, 92521, USA. jikui.song@ucr.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3AA,
C [auth D]		285Homo sapiensMutation(s): 1 
Gene Names: DNMT3A
EC: 2.1.1.37 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K1 (Homo sapiens)
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Go to UniProtKB:  Q9Y6K1
PHAROS:  Q9Y6K1
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UniProt GroupQ9Y6K1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3-likeB,
D [auth C]		209Homo sapiensMutation(s): 0 
Gene Names: DNMT3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJW3 (Homo sapiens)
Explore Q9UJW3 
Go to UniProtKB:  Q9UJW3
PHAROS:  Q9UJW3
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UniProt GroupQ9UJW3
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Entity ID: 3
MoleculeChainsLengthOrganismImage
CGT DNA (25-MER)E, F25synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
G [auth A],
H [auth D]		S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.56α = 90
b = 205.56β = 90
c = 89.505γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data 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: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references