2ZO0

mouse NP95 SRA domain DNA specific complex 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix

Hashimoto, H.Horton, J.R.Zhang, X.Bostick, M.Jacobsen, S.E.Cheng, X.

(2008) Nature 455: 826-829

  • DOI: 10.1038/nature07280
  • Primary Citation of Related Structures:  
  • Also Cited By: 3FDE, 3F8J, 3F8I

  • PubMed Abstract: 
  • Maintenance methylation of hemimethylated CpG dinucleotides at DNA replication forks is the key to faithful mitotic inheritance of genomic methylation patterns. UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for maintena ...

    Maintenance methylation of hemimethylated CpG dinucleotides at DNA replication forks is the key to faithful mitotic inheritance of genomic methylation patterns. UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for maintenance methylation by interacting with DNA nucleotide methyltransferase 1 (DNMT1), the maintenance methyltransferase, and with hemimethylated CpG, the substrate for DNMT1 (refs 1 and 2). Here we present the crystal structure of the SET and RING-associated (SRA) domain of mouse UHRF1 in complex with DNA containing a hemimethylated CpG site. The DNA is contacted in both the major and minor grooves by two loops that penetrate into the middle of the DNA helix. The 5-methylcytosine has flipped completely out of the DNA helix and is positioned in a binding pocket with planar stacking contacts, Watson-Crick polar hydrogen bonds and van der Waals interactions specific for 5-methylcytosine. Hence, UHRF1 contains a previously unknown DNA-binding module and is the first example of a non-enzymatic, sequence-specific DNA-binding protein domain to use the base flipping mechanism to interact with DNA.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase UHRF1
B
212Mus musculusMutation(s): 0 
Gene Names: Uhrf1 (Np95)
EC: 2.3.2.27
Find proteins for Q8VDF2 (Mus musculus)
Go to UniProtKB:  Q8VDF2
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3')D13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3')E13N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
E
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.982α = 90.00
b = 69.008β = 90.00
c = 92.956γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
PHASERphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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