2ZKD

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism

Arita, K.Ariyoshi, M.Tochio, H.Nakamura, Y.Shirakawa, M.

(2008) Nature 455: 818-821

  • DOI: 10.1038/nature07249
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability. Differences in DNA methylation patterns underlie ...

    DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability. Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis. Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands. The protein UHRF1 (also known as Np95 and ICBP90) recognizes hemi-methylation sites via a SET and RING-associated (SRA) domain and directs Dnmt1 to these sites. Here we report the crystal structures of the SRA domain in free and hemi-methylated DNA-bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino-terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl-CpG-binding domain, the methylcytosine base at the hemi-methylated site is flipped out of the DNA helix in the SRA-DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1.


    Organizational Affiliation

    Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase UHRF1
A, B
210Mus musculusMutation(s): 1 
Gene Names: Uhrf1 (Np95)
EC: 2.3.2.27
Find proteins for Q8VDF2 (Mus musculus)
Go to UniProtKB:  Q8VDF2
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3')C,E12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3')D,F12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
D, F
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.587α = 90.00
b = 104.036β = 99.18
c = 65.586γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance