4NM6

Crystal structure of TET2-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.026 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation.

Hu, L.Li, Z.Cheng, J.Rao, Q.Gong, W.Liu, M.Shi, Y.G.Zhu, J.Wang, P.Xu, Y.

(2013) Cell 155: 1545-1555

  • DOI: 10.1016/j.cell.2013.11.020

  • PubMed Abstract: 
  • TET proteins oxidize 5-methylcytosine (5mC) on DNA and play important roles in various biological processes. Mutations of TET2 are frequently observed in myeloid malignance. Here, we present the crystal structure of human TET2 bound to methylated DNA ...

    TET proteins oxidize 5-methylcytosine (5mC) on DNA and play important roles in various biological processes. Mutations of TET2 are frequently observed in myeloid malignance. Here, we present the crystal structure of human TET2 bound to methylated DNA at 2.02 Å resolution. The structure shows that two zinc fingers bring the Cys-rich and DSBH domains together to form a compact catalytic domain. The Cys-rich domain stabilizes the DNA above the DSBH core. TET2 specifically recognizes CpG dinucleotide and shows substrate preference for 5mC in a CpG context. 5mC is inserted into the catalytic cavity with the methyl group orientated to catalytic Fe(II) for reaction. The methyl group is not involved in TET2-DNA contacts so that the catalytic cavity allows TET2 to accommodate 5mC derivatives for further oxidation. Mutations of Fe(II)/NOG-chelating, DNA-interacting, and zinc-chelating residues are frequently observed in human cancers. Our studies provide a structural basis for understanding the mechanisms of TET-mediated 5mC oxidation.


    Organizational Affiliation

    Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylcytosine dioxygenase TET2
A
463Homo sapiensMutation(s): 0 
Gene Names: TET2 (KIAA1546)
EC: 1.14.11.n2
Find proteins for Q6N021 (Homo sapiens)
Go to Gene View: TET2
Go to UniProtKB:  Q6N021
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'B,C12N/A
Small Molecules
Ligands 3 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
FE2
Query on FE2

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Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

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Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
B, C
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.026 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 48.296α = 90.00
b = 88.186β = 90.00
c = 262.962γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Source and taxonomy