3AV4

Crystal structure of mouse DNA methyltransferase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).

Takeshita, K.Suetake, I.Yamashita, E.Suga, M.Narita, H.Nakagawa, A.Tajima, S.

(2011) Proc.Natl.Acad.Sci.USA 108: 9055-9059

  • DOI: 10.1073/pnas.1019629108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methylation of cytosine in DNA plays a crucial role in development through inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation patterns to the next generation via its preferential methylation ...

    Methylation of cytosine in DNA plays a crucial role in development through inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation patterns to the next generation via its preferential methylation of hemimethylated CpG sites in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here we report the crystal structure of the large fragment (291-1620) of mouse Dnmt1 and its complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein. Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to replication foci is inserted into the DNA-binding pocket, indicating that this domain must be removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic cysteine residue undergoes a conformation transition to a catalytically competent position. For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance methylation is a multistep process accompanied by structural changes.


    Organizational Affiliation

    Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 1
A
1330Mus musculusMutation(s): 0 
Gene Names: Dnmt1 (Dnmt, Met1, Uim)
EC: 2.1.1.37
Find proteins for P13864 (Mus musculus)
Go to UniProtKB:  P13864
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.780α = 90.00
b = 97.865β = 90.00
c = 130.636γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
BUSTER-TNTrefinement
DENZOdata reduction
SHARPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-06-27
    Type: Experimental preparation
  • Version 1.3: 2019-12-25
    Type: Database references