6F57

Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for DNMT3A-mediated de novo DNA methylation.

Zhang, Z.M.Lu, R.Wang, P.Yu, Y.Chen, D.Gao, L.Liu, S.Ji, D.Rothbart, S.B.Wang, Y.Wang, G.G.Song, J.

(2018) Nature 554: 387-391

  • DOI: 10.1038/nature25477
  • Primary Citation of Related Structures:  
    6BRR, 6F57, 5YX2

  • PubMed Abstract: 
  • DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) at cytosines is essential for genome regulation and development. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms un ...

    DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) at cytosines is essential for genome regulation and development. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms underlying DNMT3 substrate recognition and enzymatic specificity remain elusive. Here we report a 2.65-ångström crystal structure of the DNMT3A-DNMT3L-DNA complex in which two DNMT3A monomers simultaneously attack two cytosine-phosphate-guanine (CpG) dinucleotides, with the target sites separated by 14 base pairs within the same DNA duplex. The DNMT3A-DNA interaction involves a target recognition domain, a catalytic loop, and DNMT3A homodimeric interface. Arg836 of the target recognition domain makes crucial contacts with CpG, ensuring DNMT3A enzymatic preference towards CpG sites in cells. Haematological cancer-associated somatic mutations of the substrate-binding residues decrease DNMT3A activity, induce CpG hypomethylation, and promote transformation of haematopoietic cells. Together, our study reveals the mechanistic basis for DNMT3A-mediated DNA methylation and establishes its aetiological link to human disease.


    Organizational Affiliation

    Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3AAD285Homo sapiensMutation(s): 0 
Gene Names: DNMT3A
EC: 2.1.1.37
Find proteins for Q9Y6K1 (Homo sapiens)
Explore Q9Y6K1 
Go to UniProtKB:  Q9Y6K1
NIH Common Fund Data Resources
PHAROS  Q9Y6K1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3-likeBC209Homo sapiensMutation(s): 0 
Gene Names: DNMT3L
Find proteins for Q9UJW3 (Homo sapiens)
Explore Q9UJW3 
Go to UniProtKB:  Q9UJW3
NIH Common Fund Data Resources
PHAROS  Q9UJW3
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')E, G10Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')F, H11Homo sapiens
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SAH
      Query on SAH

      Download CCD File 
      A, 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: 3.10 Å
      • R-Value Free: 0.242 
      • R-Value Work: 0.211 
      • R-Value Observed: 0.213 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 176.611α = 90
      b = 49.559β = 90
      c = 162.259γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data scaling
      Cootmodel building
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2017-12-01 
      • Released Date: 2018-01-31 
      • Deposition Author(s): Zhang, Z.M., Song, J.

      Revision History 

      • Version 1.0: 2018-01-31
        Type: Initial release
      • Version 1.1: 2018-02-07
        Changes: Database references
      • Version 1.2: 2018-02-21
        Changes: Database references
      • Version 1.3: 2018-02-28
        Changes: Database references