4NM6

Crystal structure of TET2-DNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.2 of the entry. See complete history. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7NE6


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
  • Primary Citation of Related Structures:  
    4NM6

  • 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 at 2 ...

    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. Electronic address: xuyh@fudan.edu.cn.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methylcytosine dioxygenase TET2A463Homo sapiensMutation(s): 0 
Gene Names: TET2, KIAA1546, Nbla00191
EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q6N021 (Homo sapiens)
Explore Q6N021 
Go to UniProtKB:  Q6N021
PHAROS:  Q6N021
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N021
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'B, C12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA
Download Ideal Coordinates CCD File 
H [auth A]N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
G [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.296α = 90
b = 88.186β = 90
c = 262.962γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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