4DA4

Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation.

Song, J.Teplova, M.Ishibe-Murakami, S.Patel, D.J.

(2012) Science 335: 709-712

  • DOI: 10.1126/science.1214453

  • PubMed Abstract: 
  • DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containi ...

    DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containing a central hemimethylated CpG site. The methyl group of methylcytosine is positioned within a shallow hydrophobic concave surface, whereas the cytosine on the target strand is looped out and covalently anchored within the catalytic pocket. The DNA is distorted at the hemimethylated CpG step, with side chains from catalytic and recognition loops inserting through both grooves to fill an intercalation-type cavity associated with a dual base flip-out on partner strands. Structural and biochemical data establish how a combination of active and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated maintenance DNA methylation.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 1
A, B
873Mus musculusGene Names: Dnmt1 (Dnmt, Met1, Uim)
EC: 2.1.1.37
Find proteins for P13864 (Mus musculus)
Go to UniProtKB:  P13864
Entity ID: 2
MoleculeChainsLengthOrganism
DNA_UPPER_STRANDC,E12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA_LOWER_STRANDD,F12N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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Download CCD File 
B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C, E
DNA LINKINGC10 H16 N3 O7 PDC
C49
Query on C49
D, F
DNA LINKINGC10 H15 F N3 O7 P SDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.680α = 90.00
b = 152.042β = 94.54
c = 96.053γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MAR345dtbdata collection
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-01-12 
  • Released Date: 2012-02-22 
  • Deposition Author(s): Song, J., Patel, D.J.

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release